diff --git a/DESCRIPTION b/DESCRIPTION
index 962c003209c86b21808577b7d02c76e3708756c6..f8082aa95ce2577ac26073a02abace4364943155 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: mixKernel
 Type: Package
 Title: Omics Data Integration Using Kernel Methods
-Version: 0.9
-Date: 2023-09-17
+Version: 0.9-1
+Date: 2024-01-27
 Depends: R (>= 3.5.0), mixOmics, ggplot2, reticulate (>= 1.14)
 Imports: vegan, phyloseq, corrplot, psych, quadprog, LDRTools, Matrix, methods, markdown
 Suggests: rmarkdown, knitr
@@ -39,4 +39,4 @@ Config/reticulate:
       list(package = "sklearn", pip = TRUE)
     )
   )
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
diff --git a/NEWS.md b/NEWS.md
index d61ab88857bdb04cdb90e5ec1542d2154b174005..bc483600b81e673933c1acfd032036877eaef5d2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# Version 0.9-1 [2024-01-27]
+
+* fixed CRAN checks (vignettes and documentation formats)
+* properly defined tests of classes with inherits
+* fixed a bug in exports
+
 # Version 0.9 [2023-09-08]
 
 * transition to roxygen documentation and fixing the format of some files 
@@ -39,4 +45,4 @@ Devin Leopold)
 
 # Version 0.1 [2017-05-18]
 
-* Initial release
\ No newline at end of file
+* Initial release
diff --git a/R/cim.kernel.R b/R/cim.kernel.R
index fe0b510f9011f4c4c9541272660676a7e2532c2e..196a20c4e6ad9553905649933834218dbecb6e8b 100644
--- a/R/cim.kernel.R
+++ b/R/cim.kernel.R
@@ -71,8 +71,8 @@ cim.kernel <- function(..., scale = TRUE,
     stop("Each block of 'K' must have a unique name.")
   }
   # check all inputs are kernels
-  are.kernels <- unlist(lapply(K, function (k) {
-    "kernel" %in% class(k)
+  are.kernels <- unlist(lapply(K, function(k) {
+    inherits(k, "kernel")
   }))
   if (!all(are.kernels)) {
     stop("Each block of 'K' must be a kernel.")
diff --git a/R/combine.kernels.R b/R/combine.kernels.R
index 21a53809ea7021629c1afc67d09a54ba232372d0..8fa2d275633a20fe8a6f0617710e1d3bbedc06ea 100644
--- a/R/combine.kernels.R
+++ b/R/combine.kernels.R
@@ -2,17 +2,6 @@
 #' 
 #' Compute multiple kernels into a single meta-kernel
 #'
-#' @details
-#' The arguments \code{method} allows to specify the Unsupervised Multiple
-#' Kernel Learning (UMKL) method to use: \itemize{
-#'   \item{\code{"STATIS-UMKL"}}{: combines input kernels into the best 
-#'   consensus of all kernels;}
-#'   \item \code{"full-UMKL"}{: computes a kernel that minimizes the distortion 
-#'   between the meta-kernel and the k-NN graphs obtained from all input 
-#'   kernels;}
-#'   \item \code{"sparse-UMKL"}{: a sparse variant of the \code{"full-UMKL"} 
-#'   approach.}}
-#'
 #' @param ... list of kernels (called 'blocks') computed on different datasets 
 #' and measured on the same samples.
 #' @param scale boleean. If \code{scale = TRUE}, each block is standardized to 
@@ -26,14 +15,25 @@
 #' @param rho integer. Parameters for the augmented Lagrangian method. Default: 
 #' \code{20}.
 #' 
-#' @return \code{combine.kernels} returns an object of classes \code{"kernel"} and 
-#' \code{"metaKernel"}, a list that contains the following components: \itemize{
+#' @return \code{combine.kernels} returns an object of classes \code{"kernel"} 
+#' and \code{"metaKernel"}, a list that contains the following components: 
 #'   \item{kernel}{: the computed meta-kernel matrix;}
 #'   \item{X}{: the dataset from which the kernel has been computed, as given by
 #'   the function \code{\link{compute.kernel}}. Can be \code{NULL} if a kernel
 #'   matrix was passed to this function;}
 #'   \item{weights}{: a vector containing the weights used to combine the 
 #'   kernels.} 
+#'   
+#' @details
+#' The arguments \code{method} allows to specify the Unsupervised Multiple
+#' Kernel Learning (UMKL) method to use: \itemize{
+#'   \item \code{"STATIS-UMKL"}: combines input kernels into the best 
+#'   consensus of all kernels;
+#'   \item \code{"full-UMKL"}: computes a kernel that minimizes the distortion 
+#'   between the meta-kernel and the k-NN graphs obtained from all input 
+#'   kernels;
+#'   \item \code{"sparse-UMKL"}: a sparse variant of the \code{"full-UMKL"} 
+#'   approach.
 #' }
 #' 
 #' @author Jerome Mariette <jerome.mariette@@inrae.fr>
diff --git a/R/compute.kernel.R b/R/compute.kernel.R
index 06ccda4cf2176a7336125da0e6d2d53c491eebc0..c9a2262448464a24c45bd49a6a8abf25de925c3e 100644
--- a/R/compute.kernel.R
+++ b/R/compute.kernel.R
@@ -11,8 +11,7 @@
 #' \code{"gaussian.radial.basis"}, \code{"poisson"} or \code{"phylogenetic"}. 
 #' Default: \code{"linear"}.
 #' @param ... the kernel function arguments. Valid parameters for 
-#' pre-implemented kernels are: 
-#'   \itemize{
+#' pre-implemented kernels are: \itemize{
 #'     \item \code{phylogenetic.tree} (\code{"phylogenetic"}): an instance of 
 #'     phylo-class that contains a phylogenetic tree (required).
 #'     \item \code{scale} (\code{"linear"} or \code{"gaussian.radial.basis"}): 
@@ -30,7 +29,8 @@
 #'     \code{"cao"}.
 #'     \item \code{normalization} (\code{"poisson"}): character. Can be 
 #'     \code{"deseq"} (more robust), \code{"mle"} (less robust) or 
-#'     \code{"quantile"}.}
+#'     \code{"quantile"}.
+#' }
 #' @param test.pos.semidef boleean. If \code{test.pos.semidef = TRUE}, the 
 #' positive semidefiniteness of the resulting matrix is checked.
 #' 
diff --git a/R/kernel.pca.R b/R/kernel.pca.R
index bb54efaa4ce7527621af7f96a1db0e5e28a8f58e..fa6352e4715ffa94c5f657e15b6d02a3a031d399 100644
--- a/R/kernel.pca.R
+++ b/R/kernel.pca.R
@@ -7,7 +7,7 @@
 #' @param ncomp integer. Indicates the number of components to return..
 #' 
 #' @return \code{kernel.pca} returns an object of classes \code{"kernel.pca"} 
-#' and \code{"pca"}, which is a list containing the following entries: \itemize{
+#' and \code{"pca"}, which is a list containing the following entries: 
 #'   \item{ncomp}{: the number of principal components;}
 #'   \item{X}{: the input kernel matrix;} 
 #'   \item{kernel}{: the input kernel object provided by the user;}
@@ -16,7 +16,6 @@
 #'   whose columns contain the eigenvectors);}
 #'   \item{loadings}{: same as 'rotation' to keep the mixOmics spirit;}
 #'   \item{x}{: same as 'rotation' to keep the mixOmics spirit;}
-#' }
 #' 
 #' @author Jerome Mariette <jerome.mariette@@inrae.fr>
 #' Nathalie Vialaneix <nathalie.vialaneix@@inrae.fr>
@@ -33,7 +32,7 @@
 kernel.pca <- function(K, ncomp = nrow(K$kernel)) {
   
   #-- checking general input parameters --#
-  if (!"kernel" %in% class(K)) {
+  if (!inherits(K, "kernel")) {
     stop("'K' should be an instance of class 'kernel'.", call. = FALSE)
   }
   
diff --git a/R/kernel.pca.permute.R b/R/kernel.pca.permute.R
index 3469a3d0ac26c0d021be872766499940771da172..06f6fae13d40291fa781c2adc387ecc49a81a7c6 100644
--- a/R/kernel.pca.permute.R
+++ b/R/kernel.pca.permute.R
@@ -57,7 +57,7 @@ kernel.pca.permute = function(kpca.result, ncomp = 1, ..., directory = NULL) {
   permutations <- list(...)
   blocks <- names(permutations)
   
-  if (!"kernel.pca" %in% class(kpca.result)) {
+  if (!inherits(kpca.result, "kernel.pca")) {
     stop(paste0("'kpca.result' should be an instance of 'kernel.pca' object", 
                 " returned by the kernel.pca function."), call. = FALSE)
   }
@@ -68,10 +68,10 @@ kernel.pca.permute = function(kpca.result, ncomp = 1, ..., directory = NULL) {
   }
   
   # it the kpca has been performed on a meta kernel
-  is.metakernel <- "metaKernel" %in% class(kpca.result$kernel)
+  is.metakernel <- inherits(kpca.result$kernel, "metaKernel")
 
   if (is.metakernel) {
-    # test if there is no kidentity kernels, i.e. kernel with X = NULL
+    # test if there is no identity kernels, i.e. kernel with X = NULL
     sapply(blocks, function(b.label) {
       if (is.null(kpca.result$kernel$X[[b.label]]$X)) {
         stop(paste0("No permutation can be done on block '", b.label, 
diff --git a/R/plot.kernel.pca.R b/R/plot.kernel.pca.R
index 53649819a4520059258fb967390a524382c16bbe..01f3790a77712557102c041782833ec94f9a74f3 100755
--- a/R/plot.kernel.pca.R
+++ b/R/plot.kernel.pca.R
@@ -23,13 +23,13 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 #############################################################################################################
-
+#' @export
 
 plot.kernel.pca <- function(x, ncomp = min(10, x$ncomp), ...) {
     
   #-- checking general input parameters --#
 
-  if (!"kernel.pca" %in% class(x)) {
+  if (!inherits(x, "kernel.pca")) {
   	stop("'x' should be an instance of 'kernel.pca' object returned by the",
   	     " kernel.pca function.", call. = FALSE)
   }
@@ -46,5 +46,3 @@ plot.kernel.pca <- function(x, ncomp = min(10, x$ncomp), ...) {
           xlab = "Principal Components", ylab = "Explained Variance", ...)
     
 }
-
-
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..f59f372a73cbee8810cc8da6ac88ba6252cf48b6
--- /dev/null
+++ b/README.md
@@ -0,0 +1,55 @@
+mixKernel
+================
+
+Kernel-based methods are powerful methods for integrating heterogeneous
+types of data. mixKernel aims at providing methods to combine kernel for
+unsupervised exploratory analysis. Different solutions are provided to
+compute a meta-kernel, in a consensus way or in a way that best
+preserves the original topology of the data. mixKernel also integrates
+kernel PCA to visualize similarities between samples in a non linear
+space and from the multiple source point of view. Functions to select
+and display important variables are also provided in the package in an
+unsupervised and kernel association frameworks.
+
+Installation instructions are provided below.
+
+## Installation of python dependencies
+
+The following python modules are required for the functions performing
+feature selection in `mixKernel`: autograd, scipy, sklearn, numpy
+
+``` python
+pip3 install autograd
+pip3 install scipy
+pip3 install sklearn
+pip3 install numpy
+```
+
+## Installation of Bioconductor dependencies
+
+Two Bioconductor packages are required for `mixKernel` installation:
+`mixOmics` and `phyloseq`:
+
+``` r
+install.packages("BiocManager")
+BiocManager::install("mixOmics")
+BiocManager::install("phyloseq")
+```
+
+## mixKernel installation
+
+Finally the installation is completed with:
+
+``` r
+install.packages("mixKernel")
+```
+
+## References
+
+Mariette, J. and Villa-Vialaneix, N. (2018). Unsupervised multiple
+kernel learning for heterogeneous data integration. *Bioinformatics*,
+**34**(6), 1009-1015.
+
+Brouard, C., Mariette, J., Flamary, R., & Vialaneix, N. (2022). Feature
+selection for kernel methods in systems biology. *NAR Genomics and
+Bioinformatics*, **4**(1), lqac014.
diff --git a/docs/404.html b/docs/404.html
new file mode 100644
index 0000000000000000000000000000000000000000..142dff9f4d7c06f44f804755423d22796110d205
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+++ b/docs/404.html
@@ -0,0 +1,111 @@
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+Content not found. Please use links in the navbar.
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+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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+</div>
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+
+      <footer><div class="copyright">
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new file mode 100644
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+</div>
+<!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header toc-ignore">
+      <h1 data-toc-skip>Installation instruction for mixKernel</h1>
+                        <h4 data-toc-skip class="author">Jérôme Mariette, Céline Brouard, Rémi Flamary and Nathalie Vialaneix</h4>
+            
+            <h4 data-toc-skip class="date">12 janvier, 2022</h4>
+      
+      
+      <div class="hidden name"><code>0-mixKernelInstallation.Rmd</code></div>
+
+    </div>
+
+    
+    
+<!--
+%\VignetteEngine{knitr}
+%\VignetteIndexEntry{Installation instruction}
+%\VignettePackage{mixKernel}
+-->
+<p>This vignette provide installation for <code>mixKernel</code> instructions.</p>
+<div class="section level2">
+<h2 id="installation-of-python-dependencies">Installation of python dependencies<a class="anchor" aria-label="anchor" href="#installation-of-python-dependencies"></a>
+</h2>
+<p>The following python modules are required for the functions performing feature selection in <code>mixKernel</code>: autograd, scipy, sklearn, numpy</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>pip3 install autograd</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>pip3 install scipy</span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>pip3 install sklearn</span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>pip3 install numpy</span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="installation-of-bioconductor-dependencies">Installation of Bioconductor dependencies<a class="anchor" aria-label="anchor" href="#installation-of-bioconductor-dependencies"></a>
+</h2>
+<p>Two Bioconductor packages are required for <code>mixKernel</code> installation: <code>mixOmics</code> and <code>phyloseq</code>:</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span>
+<span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocManager/man/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"mixOmics"</span><span class="op">)</span>
+<span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocManager/man/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"phyloseq"</span><span class="op">)</span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="mixkernel-installation">mixKernel installation<a class="anchor" aria-label="anchor" href="#mixkernel-installation"></a>
+</h2>
+<p>Finally the installation is completed with:</p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"mixKernel"</span><span class="op">)</span></code></pre></div>
+</div>
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+
+        <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
+    </nav>
+</div>
+
+</div>
+
+
+
+      <footer><div class="copyright">
+  <p></p>
+<p>Developed by Jerome Mariette, Celine Brouard, Remi Flamary, Nathalie Vialaneix.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+</div>
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diff --git a/docs/articles/a-mixKernelInstallation.html b/docs/articles/a-mixKernelInstallation.html
new file mode 100644
index 0000000000000000000000000000000000000000..5d1b612661f5a664a83b43c7adefb5fba7129c7f
--- /dev/null
+++ b/docs/articles/a-mixKernelInstallation.html
@@ -0,0 +1,151 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>Installation instruction for mixKernel • mixKernel</title>
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
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+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+<body data-spy="scroll" data-target="#toc">
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+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">mixKernel</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.9-1</span>
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+    <div id="navbar" class="navbar-collapse collapse">
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+  <a href="../reference/index.html">Reference</a>
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+    Articles
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+  </a>
+  <ul class="dropdown-menu" role="menu">
+<li>
+      <a href="../articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="../articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul>
+<ul class="nav navbar-nav navbar-right"></ul>
+</div>
+<!--/.nav-collapse -->
+  </div>
+<!--/.container -->
+</div>
+<!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header toc-ignore">
+      <h1 data-toc-skip>Installation instruction for mixKernel</h1>
+                        <h4 data-toc-skip class="author">Jérôme
+Mariette, Céline Brouard, Rémi Flamary and Nathalie Vialaneix</h4>
+            
+            <h4 data-toc-skip class="date">27 janvier, 2024</h4>
+      
+      
+      <div class="hidden name"><code>a-mixKernelInstallation.Rmd</code></div>
+
+    </div>
+
+    
+    
+<p>This vignette provide installation for <code>mixKernel</code>
+instructions.</p>
+<div class="section level2">
+<h2 id="installation-of-python-dependencies">Installation of python dependencies<a class="anchor" aria-label="anchor" href="#installation-of-python-dependencies"></a>
+</h2>
+<p>The following python modules are required for the functions
+performing feature selection in <code>mixKernel</code>: autograd, scipy,
+sklearn, numpy</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>pip3 install autograd</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>pip3 install scipy</span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a>pip3 install sklearn</span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>pip3 install numpy</span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="installation-of-bioconductor-dependencies">Installation of Bioconductor dependencies<a class="anchor" aria-label="anchor" href="#installation-of-bioconductor-dependencies"></a>
+</h2>
+<p>Two Bioconductor packages are required for <code>mixKernel</code>
+installation: <code>mixOmics</code> and <code>phyloseq</code>:</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span></span>
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="st">"mixOmics"</span><span class="op">)</span></span>
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="st">"phyloseq"</span><span class="op">)</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="mixkernel-installation">mixKernel installation<a class="anchor" aria-label="anchor" href="#mixkernel-installation"></a>
+</h2>
+<p>Finally the installation is completed with:</p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"mixKernel"</span><span class="op">)</span></span></code></pre></div>
+</div>
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+
+        <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
+    </nav>
+</div>
+
+</div>
+
+
+
+      <footer><div class="copyright">
+  <p></p>
+<p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/articles/index.html b/docs/articles/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..edbc02b45a0ca2dd3cec108d15fa37bc2594dd40
--- /dev/null
+++ b/docs/articles/index.html
@@ -0,0 +1,85 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Articles • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">mixKernel</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.9-1</span>
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+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="../articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
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+    <div class="section ">
+      <h3>All vignettes</h3>
+      <p class="section-desc"></p>
+
+      <dl><dt><a href="a-mixKernelInstallation.html">Installation instruction for mixKernel</a></dt>
+        <dd>
+        </dd><dt><a href="mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a></dt>
+        <dd>
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+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
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diff --git a/docs/articles/mixKernelUsersGuide.html b/docs/articles/mixKernelUsersGuide.html
new file mode 100644
index 0000000000000000000000000000000000000000..08b9d307befdbb9f91b3e11e0fc129086f91f48c
--- /dev/null
+++ b/docs/articles/mixKernelUsersGuide.html
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+    <div class="page-header toc-ignore">
+      <h1 data-toc-skip>Data Integration using Unsupervised Multiple
+Kernel Learning</h1>
+                        <h4 data-toc-skip class="author">Jérôme
+Mariette, Céline Brouard, Rémi Flamary and Nathalie Vialaneix</h4>
+            
+            <h4 data-toc-skip class="date">27 janvier, 2024</h4>
+      
+      
+      <div class="hidden name"><code>mixKernelUsersGuide.Rmd</code></div>
+
+    </div>
+
+    
+    
+<div class="section level2">
+<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+</h2>
+<p>The TARA Oceans expedition facilitated the study of plankton
+communities by providing ocean metagenomic data combined with
+environmental measures to the scientific community. This study focuses
+on 139 prokaryotic-enriched samples collected from 68 stations and
+spread across three depth layers: the surface (SRF), the deep
+chlorophyll maximum (DCM) layer and the mesopelagic (MES) zones. Samples
+were located in 8 different oceans or seas: Indian Ocean (IO),
+Mediterranean Sea (MS), North Atlantic Ocean (NAO), North Pacific Ocean
+(NPO), Red Sea (RS), South Atlantic Ocean (SAO), South Pacific Ocean
+(SPO) and South Ocean (SO).</p>
+<p>In this vignette, we consider a subset of the original data analyzed
+in the article <a href="http://dx.doi.org/10.1093/bioinformatics/btx682" class="external-link">(Mariette &amp;
+Villa-Vialaneix, 2018)</a> and illustrate the usefulness of mixKernel to
+1/ perform an integrative exploratory analysis as in (Mariette &amp;
+Villa-Vialaneix, 2018) and to 2/ select relevant variables for
+unsupervised analysis.</p>
+<p>The data include 1% of the 35,650 prokaryotic OTUs and of the 39,246
+bacterial genes that were randomly selected. <strong>The aim is to
+integrate prokaryotic abundances and functional processes to
+environmental measure with an unsupervised method</strong>.</p>
+<p>Install and load the mixOmics and mixKernel packages:</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co">## required python modules: autograd, numpy, scipy, sklearn</span></span>
+<span><span class="co">## To properly install packages, run:</span></span>
+<span><span class="co"># install.packages("BiocManager")</span></span>
+<span><span class="co"># BiocManager::install("mixOmics")</span></span>
+<span><span class="co"># BiocManager::install("phyloseq")</span></span>
+<span><span class="co"># install.packages("mixKernel")</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://www.mixOmics.org" class="external-link">mixOmics</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://mixkernel.clementine.wf" class="external-link">mixKernel</a></span><span class="op">)</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="loading-tara-ocean-datasets">Loading TARA Ocean datasets<a class="anchor" aria-label="anchor" href="#loading-tara-ocean-datasets"></a>
+</h2>
+<p>The (previously normalized) datasets are provided as matrices with
+matching sample names (rownames):</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">)</span></span>
+<span><span class="co"># more details with: ?TARAOceans</span></span>
+<span><span class="co"># we check the dimension of the data:</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"phychem"</span> <span class="op">=</span> <span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span>, <span class="st">"pro.phylo"</span> <span class="op">=</span> <span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span>, </span>
+<span>            <span class="st">"pro.NOGs"</span> <span class="op">=</span> <span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.NOGs</span><span class="op">)</span>, <span class="va">dim</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## $phychem</span></span>
+<span><span class="co">## [1] 139  22</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $pro.phylo</span></span>
+<span><span class="co">## [1] 139 356</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $pro.NOGs</span></span>
+<span><span class="co">## [1] 139 638</span></span></code></pre>
+</div>
+<div class="section level2">
+<h2 id="multiple-kernel-computation">Multiple kernel computation<a class="anchor" aria-label="anchor" href="#multiple-kernel-computation"></a>
+</h2>
+<div class="section level3">
+<h3 id="individual-kernel-computation">Individual kernel computation<a class="anchor" aria-label="anchor" href="#individual-kernel-computation"></a>
+</h3>
+<p>For each input dataset, a kernel is computed using the function
+<code>compute.kernel</code> with the choice of linear, phylogenic or
+abundance kernels. A user defined function can also be provided as
+input(argument <code>kernel.func</code>, see
+<code><a href="../reference/compute.kernel.html">?compute.kernel</a></code>).</p>
+<p>The results are lists with a ‘kernel’ entry that stores the kernel
+matrix. The resulting kernels are symmetric matrices with a size equal
+to the number of observations (rows) in the input datasets.</p>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">phychem.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span>, kernel.func <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span></span>
+<span><span class="va">pro.phylo.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span>, kernel.func <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span>
+<span><span class="va">pro.NOGs.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.NOGs</span>, kernel.func <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># check dimensions</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">pro.NOGs.kernel</span><span class="op">$</span><span class="va">kernel</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## [1] 139 139</span></span></code></pre>
+<p>A general overview of the correlation structure between datasets is
+obtained as described in Mariette and Villa-Vialaneix (2018) and
+displayed using the function <code>cim.kernel</code>:</p>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/cim.kernel.html">cim.kernel</a></span><span class="op">(</span>phychem <span class="op">=</span> <span class="va">phychem.kernel</span>,</span>
+<span>           pro.phylo <span class="op">=</span> <span class="va">pro.phylo.kernel</span>,</span>
+<span>           pro.NOGs <span class="op">=</span> <span class="va">pro.NOGs.kernel</span>, </span>
+<span>           method <span class="op">=</span> <span class="st">"square"</span><span class="op">)</span></span></code></pre></div>
+<p><img src="mixKernelUsersGuide_files/figure-html/cim_kernel-1.png" width="400"></p>
+<p>The figure shows that <code>pro.phylo</code> and
+<code>pro.NOGs</code> is the most correlated pair of kernels. This
+result is expected as both kernels provide a summary of prokaryotic
+communities.</p>
+</div>
+<div class="section level3">
+<h3 id="combined-kernel-computation">Combined kernel computation<a class="anchor" aria-label="anchor" href="#combined-kernel-computation"></a>
+</h3>
+<p>The function <code>combine.kernels</code> implements 3 different
+methods for combining kernels: STATIS-UMKL, sparse-UMKL and full-UMKL
+(see more details in Mariette and Villa-Vialaneix, 2018). It returns a
+meta-kernel that can be used as an input for the function
+<code>kernel.pca</code> (kernel PCA). The three methods bring
+complementary information and must be chosen according to the research
+question.</p>
+<p>The <code>STATIS-UMKL</code> approach gives an overview on the common
+information between the different datasets. The <code>full-UMKL</code>
+computes a kernel that minimizes the distortion between all input
+kernels. The <code>sparse-UMKL</code> is a sparse variant of
+<code>full-UMKL</code> that selects the most relevant kernels in
+addition to distortion minimization.</p>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">meta.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/combine.kernels.html">combine.kernels</a></span><span class="op">(</span>phychem <span class="op">=</span> <span class="va">phychem.kernel</span>,</span>
+<span>                               pro.phylo <span class="op">=</span> <span class="va">pro.phylo.kernel</span>,</span>
+<span>                               pro.NOGs <span class="op">=</span> <span class="va">pro.NOGs.kernel</span>, </span>
+<span>                               method <span class="op">=</span> <span class="st">"full-UMKL"</span><span class="op">)</span></span></code></pre></div>
+</div>
+</div>
+<div class="section level2">
+<h2 id="exploratory-analysis-kernel-principal-component-analysis-kpca">Exploratory analysis: Kernel Principal Component Analysis
+(KPCA)<a class="anchor" aria-label="anchor" href="#exploratory-analysis-kernel-principal-component-analysis-kpca"></a>
+</h2>
+<div class="section level3">
+<h3 id="perform-kpca">Perform KPCA<a class="anchor" aria-label="anchor" href="#perform-kpca"></a>
+</h3>
+<p>A kernel PCA can be performed from the combined kernel with the
+function <code>kernel.pca``. The argument</code>ncomp` allows to choose
+how many components to extract from KPCA.</p>
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">kernel.pca.result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/kernel.pca.html">kernel.pca</a></span><span class="op">(</span><span class="va">meta.kernel</span>, ncomp <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
+<p>Sample plots using the <code>plotIndiv</code> function from
+<code>mixOmics</code>:</p>
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">all.depths</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/levels.html" class="external-link">levels</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">sample</span><span class="op">$</span><span class="va">depth</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="va">depth.pch</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">20</span>, <span class="fl">17</span>, <span class="fl">4</span>, <span class="fl">3</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/match.html" class="external-link">match</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">sample</span><span class="op">$</span><span class="va">depth</span>, <span class="va">all.depths</span><span class="op">)</span><span class="op">]</span></span>
+<span><span class="fu"><a href="https://rdrr.io/pkg/mixOmics/man/plotIndiv.html" class="external-link">plotIndiv</a></span><span class="op">(</span><span class="va">kernel.pca.result</span>,</span>
+<span>          comp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span><span class="op">)</span>,</span>
+<span>          ind.names <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>          legend <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>          group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/vector.html" class="external-link">as.vector</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">sample</span><span class="op">$</span><span class="va">ocean</span><span class="op">)</span>,</span>
+<span>          col.per.group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#f99943"</span>, <span class="st">"#44a7c4"</span>, <span class="st">"#05b052"</span>, <span class="st">"#2f6395"</span>, </span>
+<span>                            <span class="st">"#bb5352"</span>, <span class="st">"#87c242"</span>, <span class="st">"#07080a"</span>, <span class="st">"#92bbdb"</span><span class="op">)</span>,</span>
+<span>          pch <span class="op">=</span> <span class="va">depth.pch</span>,</span>
+<span>          pch.levels <span class="op">=</span> <span class="va">TARAoceans</span><span class="op">$</span><span class="va">sample</span><span class="op">$</span><span class="va">depth</span>,</span>
+<span>          legend.title <span class="op">=</span> <span class="st">"Ocean / Sea"</span>,</span>
+<span>          title <span class="op">=</span> <span class="st">"Projection of TARA Oceans stations"</span>,</span>
+<span>          size.title <span class="op">=</span> <span class="fl">10</span>,</span>
+<span>          legend.title.pch <span class="op">=</span> <span class="st">"Depth"</span><span class="op">)</span></span></code></pre></div>
+<p><img src="mixKernelUsersGuide_files/figure-html/plotIndiv_PCA-1.png" width="729.166666666667"></p>
+<p>The explained variance supported by each axis of KPCA is displayed
+with the <code>plot</code> function, and can help choosing the number of
+components in KPCA.</p>
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">kernel.pca.result</span><span class="op">)</span></span></code></pre></div>
+<p><img src="mixKernelUsersGuide_files/figure-html/tune_pca-1.png" width="729.166666666667"></p>
+<p>The first axis summarizes ~ 20% of the total variance.</p>
+</div>
+<div class="section level3">
+<h3 id="assessing-important-variables">Assessing important variables<a class="anchor" aria-label="anchor" href="#assessing-important-variables"></a>
+</h3>
+<p>Here we focus on the information summarized on the first component.
+Variable values are randomly permuted with the function
+<code>permute.kernel.pca</code>.</p>
+<p>In the following example, physical variable are permuted at the
+variable level (kernel <code>phychem</code>), OTU abundances from
+<code>pro.phylo</code> kernel are permuted at the phylum level (OTU
+phyla are stored in the second column, named <code>Phylum</code>, of the
+taxonomy annotation provided in <code>TARAoceans</code> object in the
+entry <code>taxonomy</code>) and gene abundances from
+<code>pro.NOGs</code> are permuted at the GO level (GO are provided in
+the entry <code>GO</code> of the dataset):</p>
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">taxonomy</span><span class="op">[</span> ,<span class="st">"Phylum"</span><span class="op">]</span>, <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">##  [1] Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria</span></span>
+<span><span class="co">##  [6] Cyanobacteria  Proteobacteria Proteobacteria Chloroflexi    Proteobacteria</span></span>
+<span><span class="co">## 56 Levels: Acidobacteria Actinobacteria aquifer1 Aquificae ... WCHB1-60</span></span></code></pre>
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">GO</span>, <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">##  [1] NA  NA  "K" NA  NA  "S" "S" "S" NA  "S"</span></span></code></pre>
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># here we set a seed for reproducible results with this tutorial</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">17051753</span><span class="op">)</span></span>
+<span><span class="va">kernel.pca.result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/kernel.pca.permute.html">kernel.pca.permute</a></span><span class="op">(</span><span class="va">kernel.pca.result</span>, ncomp <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>                                        phychem <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span><span class="op">)</span>,</span>
+<span>                                        pro.phylo <span class="op">=</span> <span class="va">TARAoceans</span><span class="op">$</span><span class="va">taxonomy</span><span class="op">[</span>, <span class="st">"Phylum"</span><span class="op">]</span>,</span>
+<span>                                        pro.NOGs <span class="op">=</span> <span class="va">TARAoceans</span><span class="op">$</span><span class="va">GO</span><span class="op">)</span></span></code></pre></div>
+<p>Results are displayed with the function
+<code>plotVar.kernel.pca</code>. The argument <code>ndisplay</code>
+indicates the number of variables to display for each kernel:</p>
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/plotVar.kernel.pca.html">plotVar.kernel.pca</a></span><span class="op">(</span><span class="va">kernel.pca.result</span>, ndisplay <span class="op">=</span> <span class="fl">10</span>, ncol <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span></code></pre></div>
+<p><img src="mixKernelUsersGuide_files/figure-html/display_var-1.png" width="729.166666666667"></p>
+<p><code>Proteobacteria</code> is the most important variable for the
+<code>pro.phylo</code> kernel.</p>
+<p>The relative abundance of `Proteobacteria`` is then extracted in each
+of our 139 samples, and each sample is colored according to the value of
+this variable in the KPCA projection plot:</p>
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">selected</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">taxonomy</span><span class="op">[</span>, <span class="st">"Phylum"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Proteobacteria"</span><span class="op">)</span></span>
+<span><span class="va">proteobacteria.per.sample</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/apply.html" class="external-link">apply</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span><span class="op">[</span>, <span class="va">selected</span><span class="op">]</span>, <span class="fl">1</span>, <span class="va">sum</span><span class="op">)</span> <span class="op">/</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/base/apply.html" class="external-link">apply</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span>, <span class="fl">1</span>, <span class="va">sum</span><span class="op">)</span></span>
+<span><span class="va">colfunc</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/grDevices/colorRamp.html" class="external-link">colorRampPalette</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"royalblue"</span>, <span class="st">"red"</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="va">col.proteo</span> <span class="op">&lt;-</span> <span class="fu">colfunc</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">proteobacteria.per.sample</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="va">col.proteo</span> <span class="op">&lt;-</span> <span class="va">col.proteo</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/rank.html" class="external-link">rank</a></span><span class="op">(</span><span class="va">proteobacteria.per.sample</span>, ties <span class="op">=</span> <span class="st">"first"</span><span class="op">)</span><span class="op">]</span></span>
+<span><span class="fu"><a href="https://rdrr.io/pkg/mixOmics/man/plotIndiv.html" class="external-link">plotIndiv</a></span><span class="op">(</span><span class="va">kernel.pca.result</span>,</span>
+<span>          comp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span><span class="op">)</span>,</span>
+<span>          ind.names <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>          legend <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>          col <span class="op">=</span> <span class="va">col.proteo</span>,</span>
+<span>          pch <span class="op">=</span> <span class="va">depth.pch</span>,</span>
+<span>          pch.levels <span class="op">=</span> <span class="va">TARAoceans</span><span class="op">$</span><span class="va">sample</span><span class="op">$</span><span class="va">depth</span>,</span>
+<span>          legend.title <span class="op">=</span> <span class="st">"Ocean / Sea"</span>,</span>
+<span>          title <span class="op">=</span> <span class="st">"Representation of Proteobacteria abundance"</span>,</span>
+<span>          legend.title.pch <span class="op">=</span> <span class="st">"Depth"</span><span class="op">)</span></span></code></pre></div>
+<p><img src="mixKernelUsersGuide_files/figure-html/proteobacteria_display-1.png" width="729.166666666667"></p>
+<p>Similarly, the temperature is the most important variable for the
+<code>phychem</code> kernel. The temperature values can be displayed on
+the kernel PCA projection as follows:</p>
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">col.temp</span> <span class="op">&lt;-</span> <span class="fu">colfunc</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span><span class="op">[</span>, <span class="fl">4</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="va">col.temp</span> <span class="op">&lt;-</span> <span class="va">col.temp</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/rank.html" class="external-link">rank</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span><span class="op">[</span>, <span class="fl">4</span><span class="op">]</span>, ties <span class="op">=</span> <span class="st">"first"</span><span class="op">)</span><span class="op">]</span></span>
+<span><span class="fu"><a href="https://rdrr.io/pkg/mixOmics/man/plotIndiv.html" class="external-link">plotIndiv</a></span><span class="op">(</span><span class="va">kernel.pca.result</span>,</span>
+<span>          comp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span><span class="op">)</span>,</span>
+<span>          ind.names <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>          legend <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>          col <span class="op">=</span> <span class="va">col.temp</span>,</span>
+<span>          pch <span class="op">=</span> <span class="va">depth.pch</span>,</span>
+<span>          pch.levels <span class="op">=</span> <span class="va">TARAoceans</span><span class="op">$</span><span class="va">sample</span><span class="op">$</span><span class="va">depth</span>,</span>
+<span>          legend.title <span class="op">=</span> <span class="st">"Ocean / Sea"</span>,</span>
+<span>          title <span class="op">=</span> <span class="st">"Representation of mean temperature"</span>,</span>
+<span>          legend.title.pch <span class="op">=</span> <span class="st">"Depth"</span><span class="op">)</span></span></code></pre></div>
+<p><img src="mixKernelUsersGuide_files/figure-html/temperature_display-1.png" width="729.166666666667"></p>
+</div>
+<div class="section level3">
+<h3 id="selecting-relevant-variables">Selecting relevant variables<a class="anchor" aria-label="anchor" href="#selecting-relevant-variables"></a>
+</h3>
+<p>Here, we use a feature selection approach that does not rely on any
+assumption but explicitly takes advantage of the kernel structure in an
+unsupervised fashion. The idea is to preserve at best the similarity
+structure between samples. These examples requires the installation of
+the python modules <code>autograd</code>, <code>scipy</code>,
+<code>numpy</code>, and <code>sklearn</code>. See detailed instructions
+in the installation vignette or on mixKernel website : <a href="http://mixkernel.clementine.wf" class="external-link uri">http://mixkernel.clementine.wf</a></p>
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">have_depend</span> <span class="op">&lt;-</span> <span class="fu">reticulate</span><span class="fu">::</span><span class="fu"><a href="https://rstudio.github.io/reticulate/reference/py_module_available.html" class="external-link">py_module_available</a></span><span class="op">(</span><span class="st">"autograd"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>  <span class="fu">reticulate</span><span class="fu">::</span><span class="fu"><a href="https://rstudio.github.io/reticulate/reference/py_module_available.html" class="external-link">py_module_available</a></span><span class="op">(</span><span class="st">"scipy"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>  <span class="fu">reticulate</span><span class="fu">::</span><span class="fu"><a href="https://rstudio.github.io/reticulate/reference/py_module_available.html" class="external-link">py_module_available</a></span><span class="op">(</span><span class="st">"numpy"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>  <span class="fu">reticulate</span><span class="fu">::</span><span class="fu"><a href="https://rstudio.github.io/reticulate/reference/py_module_available.html" class="external-link">py_module_available</a></span><span class="op">(</span><span class="st">"sklearn"</span><span class="op">)</span> </span></code></pre></div>
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="va">have_depend</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="va">ukfs.res</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/select.features.html">select.features</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span>, kx.func <span class="op">=</span> <span class="st">"bray"</span>, lambda <span class="op">=</span> <span class="fl">1</span>, </span>
+<span>                              keepX <span class="op">=</span> <span class="fl">5</span>, nstep <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
+<span>  <span class="va">selected</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort</a></span><span class="op">(</span><span class="va">ukfs.res</span>, decreasing <span class="op">=</span> <span class="cn">TRUE</span>, index.return <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">$</span><span class="va">ix</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span></span>
+<span>  <span class="va">TARAoceans</span><span class="op">$</span><span class="va">taxonomy</span><span class="op">[</span><span class="va">selected</span>, <span class="op">]</span></span>
+<span><span class="op">}</span></span></code></pre></div>
+<p>The <code>select.features</code> function allows to add a structure
+constraint to the variable selection. The adjacency matrix of the graph
+representing relations between OTUs can be obtained by computing the
+Pearson correlation matrix as follows:</p>
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="http://www.stats.ox.ac.uk/pub/MASS4/" class="external-link">"MASS"</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://r.igraph.org/" class="external-link">"igraph"</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st">"correlationtree"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">pro.phylo.alist</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="st">"names"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span><span class="op">)</span>, </span>
+<span>                              <span class="fu"><a href="https://rdrr.io/r/base/t.html" class="external-link">t</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="va">L</span> <span class="op">&lt;-</span> <span class="fu">mat2list</span><span class="op">(</span><span class="fu">df2mat</span><span class="op">(</span><span class="va">pro.phylo.alist</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="va">corr.mat</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="fu">cross_cor</span><span class="op">(</span><span class="va">L</span>, remove <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="va">pro.phylo.graph</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://r.igraph.org/reference/graph_from_adjacency_matrix.html" class="external-link">graph_from_adjacency_matrix</a></span><span class="op">(</span><span class="va">corr.mat</span>, </span>
+<span>                                               mode <span class="op">=</span> <span class="st">"undirected"</span>,</span>
+<span>                                               weighted <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="va">Lg</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://r.igraph.org/reference/laplacian_matrix.html" class="external-link">laplacian_matrix</a></span><span class="op">(</span><span class="va">pro.phylo.graph</span>, sparse<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="va">have_depend</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/base/load.html" class="external-link">load</a></span><span class="op">(</span>file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span>package <span class="op">=</span> <span class="st">"mixKernel"</span><span class="op">)</span>, <span class="st">"loaddata"</span>, <span class="st">"Lg.rda"</span><span class="op">)</span><span class="op">)</span></span>
+<span>  <span class="va">ukfsg.res</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/select.features.html">select.features</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span>, kx.func <span class="op">=</span> <span class="st">"bray"</span>, </span>
+<span>                               lambda <span class="op">=</span> <span class="fl">1</span>, method <span class="op">=</span> <span class="st">"graph"</span>, Lg <span class="op">=</span> <span class="va">Lg</span>, keepX <span class="op">=</span> <span class="fl">5</span>,</span>
+<span>                               nstep <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
+<span>  </span>
+<span>  <span class="va">selected</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort</a></span><span class="op">(</span><span class="va">ukfsg.res</span>, decreasing <span class="op">=</span> <span class="cn">TRUE</span>, index.return <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">$</span><span class="va">ix</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span></span>
+<span>  <span class="va">TARAoceans</span><span class="op">$</span><span class="va">taxonomy</span><span class="op">[</span><span class="va">selected</span>, <span class="op">]</span></span>
+<span><span class="op">}</span></span></code></pre></div>
+</div>
+</div>
+<div class="section level2">
+<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
+<ol style="list-style-type: decimal">
+<li><p>Mariette, J. and Villa-Vialaneix, N. (2018). Unsupervised
+multiple kernel learning for heterogeneous data integration.
+<em>Bioinformatics</em>, <strong>34</strong>(6), 1009-1015.</p></li>
+<li><p>Zhuang, J., Wang, J., Hoi, S., and Lan, X. (2011). Unsupervised
+multiple kernel clustering. <em>Journal of Machine Learning
+Research</em> (Workshop and Conference Proceedings),
+<strong>20</strong>, 129–144.</p></li>
+<li><p>Lavit, C., Escoufier, Y., Sabatier, R., and Traissac, P. (1994).
+The act (statis method). <em>Computational Statistics &amp; Data
+Analysis</em>, <strong>18</strong>(1), 97–119.</p></li>
+</ol>
+</div>
+<div class="section level2">
+<h2 id="session-information">Session information<a class="anchor" aria-label="anchor" href="#session-information"></a>
+</h2>
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## R version 4.3.2 (2023-10-31)</span></span>
+<span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span>
+<span><span class="co">## Running under: Ubuntu 22.04.3 LTS</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Matrix products: default</span></span>
+<span><span class="co">## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 </span></span>
+<span><span class="co">## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## locale:</span></span>
+<span><span class="co">##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              </span></span>
+<span><span class="co">##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8    </span></span>
+<span><span class="co">##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   </span></span>
+<span><span class="co">##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 </span></span>
+<span><span class="co">##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            </span></span>
+<span><span class="co">## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## time zone: Europe/Paris</span></span>
+<span><span class="co">## tzcode source: system (glibc)</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## attached base packages:</span></span>
+<span><span class="co">## [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## other attached packages:</span></span>
+<span><span class="co">## [1] mixKernel_0.9-1   reticulate_1.34.0 mixOmics_6.26.0   ggplot2_3.4.4    </span></span>
+<span><span class="co">## [5] lattice_0.22-5    MASS_7.3-60.0.1  </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## loaded via a namespace (and not attached):</span></span>
+<span><span class="co">##   [1] mnormt_2.1.1            bitops_1.0-7            gridExtra_2.3          </span></span>
+<span><span class="co">##   [4] permute_0.9-7           rlang_1.1.3             magrittr_2.0.3         </span></span>
+<span><span class="co">##   [7] ade4_1.7-22             matrixStats_1.2.0       compiler_4.3.2         </span></span>
+<span><span class="co">##  [10] mgcv_1.9-1              png_0.1-8               systemfonts_1.0.5      </span></span>
+<span><span class="co">##  [13] vctrs_0.6.5             reshape2_1.4.4          quadprog_1.5-8         </span></span>
+<span><span class="co">##  [16] stringr_1.5.1           pkgconfig_2.0.3         crayon_1.5.2           </span></span>
+<span><span class="co">##  [19] fastmap_1.1.1           XVector_0.42.0          labeling_0.4.3         </span></span>
+<span><span class="co">##  [22] utf8_1.2.4              rmarkdown_2.25          markdown_1.12          </span></span>
+<span><span class="co">##  [25] ragg_1.2.7              purrr_1.0.2             xfun_0.41              </span></span>
+<span><span class="co">##  [28] zlibbioc_1.48.0         cachem_1.0.8            GenomeInfoDb_1.38.5    </span></span>
+<span><span class="co">##  [31] jsonlite_1.8.8          biomformat_1.30.0       highr_0.10             </span></span>
+<span><span class="co">##  [34] rhdf5filters_1.14.1     Rhdf5lib_1.24.1         BiocParallel_1.36.0    </span></span>
+<span><span class="co">##  [37] psych_2.4.1             parallel_4.3.2          cluster_2.1.6          </span></span>
+<span><span class="co">##  [40] R6_2.5.1                bslib_0.6.1             stringi_1.8.3          </span></span>
+<span><span class="co">##  [43] RColorBrewer_1.1-3      jquerylib_0.1.4         Rcpp_1.0.12            </span></span>
+<span><span class="co">##  [46] iterators_1.0.14        knitr_1.45              IRanges_2.36.0         </span></span>
+<span><span class="co">##  [49] Matrix_1.6-5            splines_4.3.2           igraph_1.6.0           </span></span>
+<span><span class="co">##  [52] tidyselect_1.2.0        rstudioapi_0.15.0       yaml_2.3.8             </span></span>
+<span><span class="co">##  [55] vegan_2.6-4             codetools_0.2-19        tibble_3.2.1           </span></span>
+<span><span class="co">##  [58] plyr_1.8.9              Biobase_2.62.0          withr_3.0.0            </span></span>
+<span><span class="co">##  [61] rARPACK_0.11-0          evaluate_0.23           desc_1.4.3             </span></span>
+<span><span class="co">##  [64] survival_3.5-7          Biostrings_2.70.1       pillar_1.9.0           </span></span>
+<span><span class="co">##  [67] phyloseq_1.46.0         corrplot_0.92           foreach_1.5.2          </span></span>
+<span><span class="co">##  [70] stats4_4.3.2            ellipse_0.5.0           generics_0.1.3         </span></span>
+<span><span class="co">##  [73] rprojroot_2.0.4         RCurl_1.98-1.14         S4Vectors_0.40.2       </span></span>
+<span><span class="co">##  [76] munsell_0.5.0           scales_1.3.0            glue_1.7.0             </span></span>
+<span><span class="co">##  [79] tools_4.3.2             data.table_1.14.10      RSpectra_0.16-1        </span></span>
+<span><span class="co">##  [82] fs_1.6.3                rhdf5_2.46.1            grid_4.3.2             </span></span>
+<span><span class="co">##  [85] tidyr_1.3.0             ape_5.7-1               colorspace_2.1-0       </span></span>
+<span><span class="co">##  [88] nlme_3.1-164            GenomeInfoDbData_1.2.11 cli_3.6.2              </span></span>
+<span><span class="co">##  [91] rappdirs_0.3.3          textshaping_0.3.7       fansi_1.0.6            </span></span>
+<span><span class="co">##  [94] dplyr_1.1.4             corpcor_1.6.10          gtable_0.3.4           </span></span>
+<span><span class="co">##  [97] sass_0.4.8              digest_0.6.34           BiocGenerics_0.48.1    </span></span>
+<span><span class="co">## [100] ggrepel_0.9.5           farver_2.1.1            LDRTools_0.2-2         </span></span>
+<span><span class="co">## [103] memoise_2.0.1           htmltools_0.5.7         pkgdown_2.0.7          </span></span>
+<span><span class="co">## [106] multtest_2.58.0         lifecycle_1.0.4         here_1.0.1</span></span></code></pre>
+</div>
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+
+        <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
+    </nav>
+</div>
+
+</div>
+
+
+
+      <footer><div class="copyright">
+  <p></p>
+<p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
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+</div>
+
+  
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+
+  
+
+  </body>
+</html>
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diff --git a/docs/authors.html b/docs/authors.html
new file mode 100644
index 0000000000000000000000000000000000000000..61e4f939cd3f69dec8bc0e0aa6fe7965ba940d4b
--- /dev/null
+++ b/docs/authors.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Authors and Citation • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-citation-authors">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
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+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="index.html">mixKernel</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.9-1</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="contents col-md-9">
+    <div class="section level2 authors-section">
+      <div class="page-header">
+        <h1>Authors</h1>
+      </div>
+
+      
+      <ul class="list-unstyled"><li>
+          <p><strong>Nathalie Vialaneix</strong>. Author, maintainer. 
+          </p>
+        </li>
+        <li>
+          <p><strong>Celine Brouard</strong>. Author. 
+          </p>
+        </li>
+        <li>
+          <p><strong>Remi Flamary</strong>. Author. 
+          </p>
+        </li>
+        <li>
+          <p><strong>Julien Henry</strong>. Author. 
+          </p>
+        </li>
+        <li>
+          <p><strong>Jerome Mariette</strong>. Author. 
+          </p>
+        </li>
+      </ul></div>
+    <div class="section level2 citation-section">
+    <div>
+      <h1 id="citation">Citation</h1>
+      
+    </div>
+    </div>
+
+
+    <p>Mariette J. and Villa-Vialaneix N. (2017) Unsupervised multiple kernel learning for heterogeneous data integration. Bioinformatics, 34(6): 1009-1015.</p>
+    <pre>@Article{,
+  author = {{Mariette} and {Jerome} and {Villa-Vialaneix} and {Nathalie}},
+  title = {Unsupervised multiple kernel learning for heterogeneous data integration},
+  journal = {Bioinformatics},
+  year = {2018},
+  volume = {34},
+  issue = {6},
+  pages = {1009-1015},
+  doi = {10.1093/bioinformatics/btx682},
+}</pre>
+    <p>Brouard C., Mariette J., Flamary R., Vialaneix, N. (2022) Feature selection for kernel methods in systems biology. NAR Genomics and Bioinformatics. 4(1).</p>
+    <pre>@Article{,
+  author = {Celine Brouard and Jerome Mariette and Remi Flamary and Nathalie Vialaneix},
+  title = {Feature selection for kernel methods in systems biology},
+  journal = {NAR Genomics and Bioinformatics},
+  year = {2022},
+  volume = {4},
+  issue = {1},
+  number = {lqac014},
+  doi = {10.1093/nargab/lqac014},
+}</pre>
+
+  </div>
+
+</div>
+
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
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+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css
new file mode 100644
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+++ b/docs/bootstrap-toc.css
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+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
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+/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
+
+/* All levels of nav */
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+}
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+nav[data-toggle='toc'] .nav > li > a:focus {
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+}
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
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+  color: #563d7c;
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+  border-left: 2px solid #563d7c;
+}
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+/* Nav: second level (shown on .active) */
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+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
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+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
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+  font-weight: 500;
+}
+
+/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
+nav[data-toggle='toc'] .nav > .active > ul {
+  display: block;
+}
diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js
new file mode 100644
index 0000000000000000000000000000000000000000..1cdd573b20f53b3ebe31c021e154c4338ca456af
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+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
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index 0000000000000000000000000000000000000000..e5f1fe1dfa2c34c51fe941829b511acd8c763301
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+}
+
+.algolia-autocomplete .ds-dropdown-menu {
+  width: 100%;
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+  background-color: #fff;
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+  border: 1px solid rgba(0, 0, 0, .1);
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+}
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+}
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+  border: 0;
+  max-height: 80vh;
+}
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+.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
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+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion {
+  padding: 0;
+  overflow: visible
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
+  padding: .125rem 1rem;
+  margin-top: 0;
+  font-size: 1.3em;
+  font-weight: 500;
+  color: #00008B;
+  border-bottom: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
+    float: none;
+    padding-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
+  float: none;
+  width: auto;
+  padding: 0;
+  text-align: left
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content {
+  float: none;
+  width: auto;
+  padding: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
+  display: none
+}
+
+.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
+  padding-top: .75rem;
+  margin-top: .75rem;
+  border-top: 1px solid rgba(0, 0, 0, .1)
+}
+
+.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+  display: block;
+  padding: .1rem 1rem;
+  margin-bottom: 0.1;
+  font-size: 1.0em;
+  font-weight: 400
+  /* display: none */
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--title {
+  display: block;
+  padding: .25rem 1rem;
+  margin-bottom: 0;
+  font-size: 0.9em;
+  font-weight: 400
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text {
+  padding: 0 1rem .5rem;
+  margin-top: -.25rem;
+  font-size: 0.8em;
+  font-weight: 400;
+  line-height: 1.25
+}
+
+.algolia-autocomplete .algolia-docsearch-footer {
+  width: 110px;
+  height: 20px;
+  z-index: 3;
+  margin-top: 10.66667px;
+  float: right;
+  font-size: 0;
+  line-height: 0;
+}
+
+.algolia-autocomplete .algolia-docsearch-footer--logo {
+  background-image: url("data:image/svg+xml;utf8,<svg viewBox='0 0 130 18' xmlns='http://www.w3.org/2000/svg'><defs><linearGradient x1='-36.868%' y1='134.936%' x2='129.432%' y2='-27.7%' id='a'><stop stop-color='%2300AEFF' offset='0%'/><stop stop-color='%233369E7' offset='100%'/></linearGradient></defs><g fill='none' fill-rule='evenodd'><path d='M59.399.022h13.299a2.372 2.372 0 0 1 2.377 2.364V15.62a2.372 2.372 0 0 1-2.377 2.364H59.399a2.372 2.372 0 0 1-2.377-2.364V2.381A2.368 2.368 0 0 1 59.399.022z' fill='url(%23a)'/><path d='M66.257 4.56c-2.815 0-5.1 2.272-5.1 5.078 0 2.806 2.284 5.072 5.1 5.072 2.815 0 5.1-2.272 5.1-5.078 0-2.806-2.279-5.072-5.1-5.072zm0 8.652c-1.983 0-3.593-1.602-3.593-3.574 0-1.972 1.61-3.574 3.593-3.574 1.983 0 3.593 1.602 3.593 3.574a3.582 3.582 0 0 1-3.593 3.574zm0-6.418v2.664c0 .076.082.131.153.093l2.377-1.226c.055-.027.071-.093.044-.147a2.96 2.96 0 0 0-2.465-1.487c-.055 0-.11.044-.11.104l.001-.001zm-3.33-1.956l-.312-.311a.783.783 0 0 0-1.106 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+  background-repeat: no-repeat;
+  background-position: 50%;
+  background-size: 100%;
+  overflow: hidden;
+  text-indent: -9000px;
+  width: 100%;
+  height: 100%;
+  display: block;
+  transform: translate(-8px);
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
+  color: #FF8C00;
+  background: rgba(232, 189, 54, 0.1)
+}
+
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+}
+
+.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, .15)
+}
diff --git a/docs/docsearch.js b/docs/docsearch.js
new file mode 100644
index 0000000000000000000000000000000000000000..b35504cd3a282816130a16881f3ebeead9c1bcb4
--- /dev/null
+++ b/docs/docsearch.js
@@ -0,0 +1,85 @@
+$(function() {
+
+  // register a handler to move the focus to the search bar
+  // upon pressing shift + "/" (i.e. "?")
+  $(document).on('keydown', function(e) {
+    if (e.shiftKey && e.keyCode == 191) {
+      e.preventDefault();
+      $("#search-input").focus();
+    }
+  });
+
+  $(document).ready(function() {
+    // do keyword highlighting
+    /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
+    var mark = function() {
+
+      var referrer = document.URL ;
+      var paramKey = "q" ;
+
+      if (referrer.indexOf("?") !== -1) {
+        var qs = referrer.substr(referrer.indexOf('?') + 1);
+        var qs_noanchor = qs.split('#')[0];
+        var qsa = qs_noanchor.split('&');
+        var keyword = "";
+
+        for (var i = 0; i < qsa.length; i++) {
+          var currentParam = qsa[i].split('=');
+
+          if (currentParam.length !== 2) {
+            continue;
+          }
+
+          if (currentParam[0] == paramKey) {
+            keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
+          }
+        }
+
+        if (keyword !== "") {
+          $(".contents").unmark({
+            done: function() {
+              $(".contents").mark(keyword);
+            }
+          });
+        }
+      }
+    };
+
+    mark();
+  });
+});
+
+/* Search term highlighting ------------------------------*/
+
+function matchedWords(hit) {
+  var words = [];
+
+  var hierarchy = hit._highlightResult.hierarchy;
+  // loop to fetch from lvl0, lvl1, etc.
+  for (var idx in hierarchy) {
+    words = words.concat(hierarchy[idx].matchedWords);
+  }
+
+  var content = hit._highlightResult.content;
+  if (content) {
+    words = words.concat(content.matchedWords);
+  }
+
+  // return unique words
+  var words_uniq = [...new Set(words)];
+  return words_uniq;
+}
+
+function updateHitURL(hit) {
+
+  var words = matchedWords(hit);
+  var url = "";
+
+  if (hit.anchor) {
+    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+  } else {
+    url = hit.url + '?q=' + escape(words.join(" "));
+  }
+
+  return url;
+}
diff --git a/docs/index.html b/docs/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..74e4bfabdb30aeb023f94b3cecd0b124730d0d8c
--- /dev/null
+++ b/docs/index.html
@@ -0,0 +1,184 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>Omics Data Integration Using Kernel Methods • mixKernel</title>
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
+<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<script src="pkgdown.js"></script><meta property="og:title" content="Omics Data Integration Using Kernel Methods">
+<meta property="og:description" content="Kernel-based methods are powerful methods for integrating 
+    heterogeneous types of data. mixKernel aims at providing methods to combine
+    kernel for unsupervised exploratory analysis. Different solutions are 
+    provided to compute a meta-kernel, in a consensus way or in a way that 
+    best preserves the original topology of the data. mixKernel also integrates
+    kernel PCA to visualize similarities between samples in a non linear space
+    and from the multiple source point of view 
+    &lt;doi:10.1093/bioinformatics/btx682&gt;. A method to select (as well as 
+    funtions to display) important variables is also provided 
+    &lt;doi:10.1093/nargab/lqac014&gt;.">
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+</head>
+<body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-home">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="index.html">mixKernel</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.9-1</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+<li>
+  <a href="reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+<li>
+      <a href="articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul>
+</li>
+<li>
+  <a href="news/index.html">Changelog</a>
+</li>
+      </ul>
+<ul class="nav navbar-nav navbar-right"></ul>
+</div>
+<!--/.nav-collapse -->
+  </div>
+<!--/.container -->
+</div>
+<!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="contents col-md-9">
+<div class="section level1">
+<div class="page-header"><h1 id="mixkernel">mixKernel<a class="anchor" aria-label="anchor" href="#mixkernel"></a>
+</h1></div>
+<p>Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to select and display important variables are also provided in the package in an unsupervised and kernel association frameworks.</p>
+<p>Installation instructions are provided below.</p>
+<div class="section level2">
+<h2 id="installation-of-python-dependencies">Installation of python dependencies<a class="anchor" aria-label="anchor" href="#installation-of-python-dependencies"></a>
+</h2>
+<p>The following python modules are required for the functions performing feature selection in <code>mixKernel</code>: autograd, scipy, sklearn, numpy</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>pip3 install autograd</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>pip3 install scipy</span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a>pip3 install sklearn</span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>pip3 install numpy</span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="installation-of-bioconductor-dependencies">Installation of Bioconductor dependencies<a class="anchor" aria-label="anchor" href="#installation-of-bioconductor-dependencies"></a>
+</h2>
+<p>Two Bioconductor packages are required for <code>mixKernel</code> installation: <code>mixOmics</code> and <code>phyloseq</code>:</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span></span>
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="st">"mixOmics"</span><span class="op">)</span></span>
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="st">"phyloseq"</span><span class="op">)</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="mixkernel-installation">mixKernel installation<a class="anchor" aria-label="anchor" href="#mixkernel-installation"></a>
+</h2>
+<p>Finally the installation is completed with:</p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"mixKernel"</span><span class="op">)</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
+<p>Mariette, J. and Villa-Vialaneix, N. (2018). Unsupervised multiple kernel learning for heterogeneous data integration. <em>Bioinformatics</em>, <strong>34</strong>(6), 1009-1015.</p>
+<p>Brouard, C., Mariette, J., Flamary, R., &amp; Vialaneix, N. (2022). Feature selection for kernel methods in systems biology. <em>NAR Genomics and Bioinformatics</em>, <strong>4</strong>(1), lqac014.</p>
+</div>
+</div>
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <div class="links">
+<h2 data-toc-skip>Links</h2>
+<ul class="list-unstyled">
+<li><a href="https://cloud.r-project.org/package=mixKernel" class="external-link">View on CRAN</a></li>
+<li><a href="https://forgemia.inra.fr/genotoul-bioinfo/mixKernel/-/issues" class="external-link">Report a bug</a></li>
+</ul>
+</div>
+
+<div class="license">
+<h2 data-toc-skip>License</h2>
+<ul class="list-unstyled">
+<li>GPL (&gt;= 2)</li>
+</ul>
+</div>
+
+
+<div class="citation">
+<h2 data-toc-skip>Citation</h2>
+<ul class="list-unstyled">
+<li><a href="authors.html#citation">Citing mixKernel</a></li>
+</ul>
+</div>
+
+<div class="developers">
+<h2 data-toc-skip>Developers</h2>
+<ul class="list-unstyled">
+<li>Nathalie Vialaneix <br><small class="roles"> Author, maintainer </small>  </li>
+<li>Celine Brouard <br><small class="roles"> Author </small>  </li>
+<li>Remi Flamary <br><small class="roles"> Author </small>  </li>
+<li>Julien Henry <br><small class="roles"> Author </small>  </li>
+<li>Jerome Mariette <br><small class="roles"> Author </small>  </li>
+</ul>
+</div>
+
+
+
+  </div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p>
+<p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+      </footer>
+</div>
+
+  
+
+
+  
+
+  </body>
+</html>
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diff --git a/docs/news/index.html b/docs/news/index.html
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+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Changelog • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+        <a class="navbar-link" href="../index.html">mixKernel</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.9-1</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
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+  <a href="../reference/index.html">Reference</a>
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+    Articles
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+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="../articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+      <h1 data-toc-skip>Changelog <small></small></h1>
+      
+    </div>
+
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.9-1" id="version-09-1-2024-01-27">Version 0.9-1 [2024-01-27]<small>2024-01-27</small><a class="anchor" aria-label="anchor" href="#version-09-1-2024-01-27"></a></h2>
+<ul><li>fixed CRAN checks (vignettes and documentation formats)</li>
+<li>properly defined tests of classes with inherits</li>
+<li>fixed a bug in exports</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.9" id="version-09-2023-09-08">Version 0.9 [2023-09-08]<small>2023-09-18</small><a class="anchor" aria-label="anchor" href="#version-09-2023-09-08"></a></h2>
+<ul><li>transition to roxygen documentation and fixing the format of some files (CITATION, NEWS, …)</li>
+<li>updated references</li>
+<li>new maintainer</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.8" id="version-08-2022-01-13">Version 0.8 [2022-01-13]<small>2022-01-13</small><a class="anchor" aria-label="anchor" href="#version-08-2022-01-13"></a></h2>
+<ul><li>improved documentation and added installation instructions</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.7" id="version-07-2021-06-15">Version 0.7 [2021-06-15]<small>2021-06-15</small><a class="anchor" aria-label="anchor" href="#version-07-2021-06-15"></a></h2>
+<ul><li>fix a compatibility bug of the PCA object read by mixOmics</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.6" id="version-06-2021-05-17">Version 0.6 [2021-05-17]<small>2021-05-17</small><a class="anchor" aria-label="anchor" href="#version-06-2021-05-17"></a></h2>
+<ul><li>improve mixKernel and SOMbrero compatibility</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.5" id="version-05-2021-03-01">Version 0.5 [2021-03-01]<small>2021-03-30</small><a class="anchor" aria-label="anchor" href="#version-05-2021-03-01"></a></h2>
+<ul><li>the select.features function has been added. This function replace the ukfs function and provides a supervised feature selection method based on the kernel framwork</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.4" id="version-04-2020-02-20">Version 0.4 [2020-02-20]<small>2020-02-26</small><a class="anchor" aria-label="anchor" href="#version-04-2020-02-20"></a></h2>
+<ul><li>the ukfs function has been added. This function aims at selecting relevant variables using unsupervised kernel method</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.3" id="version-03-2018-11-26">Version 0.3 [2018-11-26]<small>2018-11-26</small><a class="anchor" aria-label="anchor" href="#version-03-2018-11-26"></a></h2>
+<ul><li>fix a bug in kernel.pca.permute with duplicated block variables (reported by Devin Leopold)</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.2" id="version-02-2017-10-17">Version 0.2 [2017-10-17]<small>2018-09-11</small><a class="anchor" aria-label="anchor" href="#version-02-2017-10-17"></a></h2>
+<ul><li>Additional kernels: gaussian.radial.basis, poisson</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.1" id="version-01-2017-05-18">Version 0.1 [2017-05-18]<small>2017-05-18</small><a class="anchor" aria-label="anchor" href="#version-01-2017-05-18"></a></h2>
+<ul><li>Initial release</li>
+</ul></div>
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
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+articles:
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diff --git a/docs/reference/TARAoceans.html b/docs/reference/TARAoceans.html
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+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>TARA ocean microbiome data — TARAoceans • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="TARA ocean microbiome data — TARAoceans"><meta property="og:description" content="The TARA Oceans expedition facilitated the study of plankton communities by 
+providing oceans metagenomic data combined with environmental measures to the 
+scientific community. This dataset focuses on 139 prokaryotic-enriched 
+samples collected from 68 stations and spread across three depth layers: the 
+surface (SRF), the deep chlorophyll maximum (DCM) layer and the mesopelagic 
+(MES) zones. Samples were located in height different oceans or seas: Indian 
+Ocean (IO), Mediterranean Sea (MS), North Atlantic Ocean (NAO), North Pacific
+Ocean (NPO), Red Sea (RS), South Atlantic Ocean (SAO), South Pacific Ocean 
+(SPO) and South Ocean (SO). Here, only a subset of the original data is 
+provided (1% of the 35,650 prokaryotic operational taxonomic units (OTUs) 
+and of the 39,246 bacterial genes (NOGs) (selected at random)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>TARA ocean microbiome data</h1>
+    
+    <div class="hidden name"><code>TARAoceans.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>The TARA Oceans expedition facilitated the study of plankton communities by 
+providing oceans metagenomic data combined with environmental measures to the 
+scientific community. This dataset focuses on 139 prokaryotic-enriched 
+samples collected from 68 stations and spread across three depth layers: the 
+surface (SRF), the deep chlorophyll maximum (DCM) layer and the mesopelagic 
+(MES) zones. Samples were located in height different oceans or seas: Indian 
+Ocean (IO), Mediterranean Sea (MS), North Atlantic Ocean (NAO), North Pacific
+Ocean (NPO), Red Sea (RS), South Atlantic Ocean (SAO), South Pacific Ocean 
+(SPO) and South Ocean (SO). Here, only a subset of the original data is 
+provided (1% of the 35,650 prokaryotic operational taxonomic units (OTUs) 
+and of the 39,246 bacterial genes (NOGs) (selected at random).</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="format">
+    <h2>Format</h2>
+    <p>A list containing the following components:</p><dl><dt><code>phychem</code></dt>
+<dd><p>data matrix with 139 rows and 22 columns. Each row 
+    represents a sample and each column an environmental variable.</p></dd>
+
+  <dt><code>pro.phylo</code></dt>
+<dd><p>data matrix with 139 rows (samples) and 356 columns
+    (prokaryotic OTUs).</p></dd>
+
+  <dt><code>taxonomy</code></dt>
+<dd><p>data matrix with 356 rows (prokaryotic OTUs) and 6 
+    columns indicating the taxonomy of each OTU.</p></dd>
+
+  <dt><code>phylogenetic.tree</code></dt>
+<dd><p>a phylo object (see package 'ape') 
+    representing the prokaryotic OTUs phylogenetic tree.</p></dd>
+
+  <dt><code>pro.NOGs</code></dt>
+<dd><p>data matrix with 139 rows (samples) and 638 columns 
+    (NOGs).</p></dd>
+
+  <dt><code>sample</code></dt>
+<dd><p>a list containing three following entries (all three 
+    are character vectors): <code>name</code> (sample name), <code>ocean</code> (oceanic 
+   region of the sample) and <code>depth</code> (sample depth).</p></dd>
+
+
+</dl></div>
+    <div id="source">
+    <h2>Source</h2>
+    <p>The raw data were downloaded from 
+<a href="http://ocean-microbiome.embl.de/companion.html" class="external-link">http://ocean-microbiome.embl.de/companion.html</a>.</p>
+    </div>
+    <div id="references">
+    <h2>References</h2>
+    <p>Sunagawa S., Coelho L.P., Chaffron S., Kultima J.R., Labadie K., 
+Salazar F., Djahanschiri B., Zeller G., Mende D.R., Alberti A., 
+Cornejo-Castillo F., Costea P.I., Cruaud C., d'Oviedo F., Engelen S., 
+Ferrera I., Gasol J., Guidi L., Hildebrand F., Kokoszka F., Lepoivre C., 
+Lima-Mendez G., Poulain J., Poulos B., Royo-Llonch M., Sarmento H., 
+Vieira-Silva S., Dimier C., Picheral M., Searson S., Kandels-Lewis S., 
+<em>Tara</em> Oceans coordinators, Bowler C., de Vargas C., Gorsky G., 
+Grimsley N., Hingamp P., Iudicone D., Jaillon O., Not F., Ogata H., Pesant 
+S., Speich S., Stemmann L., Sullivan M., Weissenbach J., Wincker P., Karsenti 
+E., Raes J., Acinas S. and Bork P. (2015). Structure and function of the 
+global ocean microbiome. <em>Science</em>, <b>348</b>, 6237.</p>
+    </div>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
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+
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+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/center.scale.html b/docs/reference/center.scale.html
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@@ -0,0 +1,122 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Center and scale — center.scale • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Center and scale — center.scale"><meta property="og:description" content="Center and scale a dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+        <a class="navbar-link" href="../index.html">mixKernel</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.9-1</span>
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+    <div id="navbar" class="navbar-collapse collapse">
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+  <a href="../reference/index.html">Reference</a>
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+    Articles
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+      <a href="../articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="../articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
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+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Center and scale</h1>
+    
+    <div class="hidden name"><code>center.scale.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Center and scale a dataset.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">center.scale</span><span class="op">(</span><span class="va">X</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>X</dt>
+<dd><p>a numeric matrix (or data frame) to center and scaled.
+<code>NA</code>s not allowed.</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p><code>center.scale</code> returns a centered and scaled matrix.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code><a href="compute.kernel.html">compute.kernel</a></code>, <code><a href="combine.kernels.html">combine.kernels</a></code></p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Celine Brouard &lt;celine.brouard@inrae.fr&gt;
+Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"nutrimouse"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span> <span class="va">nutrimouse.sc</span> <span class="op">&lt;-</span> <span class="fu">center.scale</span><span class="op">(</span><span class="va">nutrimouse</span><span class="op">$</span><span class="va">gene</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
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+
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+  
+
+  </body></html>
+
diff --git a/docs/reference/cim.kernel-1.png b/docs/reference/cim.kernel-1.png
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@@ -0,0 +1,169 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute and display similarities between multiple kernels — cim.kernel • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute and display similarities between multiple kernels — cim.kernel"><meta property="og:description" content="Compute cosine from Frobenius norm between kernels and display the 
+corresponding correlation plot."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
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+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+        <a class="navbar-link" href="../index.html">mixKernel</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.9-1</span>
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+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Reference</a>
+</li>
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+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
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+  </a>
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+      <a href="../articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="../articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Compute and display similarities between multiple kernels</h1>
+    
+    <div class="hidden name"><code>cim.kernel.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Compute cosine from Frobenius norm between kernels and display the 
+corresponding correlation plot.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cim.kernel</span><span class="op">(</span></span>
+<span>  <span class="va">...</span>,</span>
+<span>  scale <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"circle"</span>, <span class="st">"square"</span>, <span class="st">"number"</span>, <span class="st">"shade"</span>, <span class="st">"color"</span>, <span class="st">"pie"</span><span class="op">)</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>...</dt>
+<dd><p>list of kernels (called 'blocks') computed on different datasets 
+and measured on the same samples.</p></dd>
+
+
+<dt>scale</dt>
+<dd><p>boleean. If <code>scale = TRUE</code>, each block is standardized to 
+zero mean and unit variance and cosine normalization is performed on the 
+kernel. Default: <code>TRUE</code>.</p></dd>
+
+
+<dt>method</dt>
+<dd><p>character. The visualization method to be used. Currently, 
+seven methods are supported (see Details).</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p><code>cim.kernel</code> returns a matrix containing the cosine from 
+Frobenius norm between kernels.</p>
+    </div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>The displayed similarities are the kernel generalization of the 
+RV-coefficient described in Lavit <em>et al.</em>, 1994.</p>
+<p>The plot is displayed using the <code><a href="https://rdrr.io/pkg/corrplot/man/corrplot.html" class="external-link">corrplot</a></code> package. 
+Seven visualization methods are implemented: <code>"circle"</code> (default), 
+<code>"square"</code>, <code>"number"</code>, <code>"pie"</code>, <code>"shade"</code> and 
+<code>"color"</code>. Circle and square areas are proportional to the absolute 
+value of corresponding similarities coefficients.</p>
+    </div>
+    <div id="references">
+    <h2>References</h2>
+    <p>Lavit C., Escoufier Y., Sabatier R. and Traissac P. (1994). The 
+ACT (STATIS method). <em>Computational Statistics and Data Analysis</em>, 
+<b>18</b>(1), 97-119.</p>
+<p>Mariette J. and Villa-Vialaneix N. (2018). Unsupervised multiple kernel 
+learning for heterogeneous data integration. <em>Bioinformatics</em>, 
+<b>34</b>(6), 1009-1015.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code><a href="compute.kernel.html">compute.kernel</a></code></p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># compute one kernel per dataset</span></span></span>
+<span class="r-in"><span><span class="va">phychem.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span>, kernel.func <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">pro.phylo.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span>, </span></span>
+<span class="r-in"><span>                                   kernel.func <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">pro.NOGs.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.NOGs</span>, </span></span>
+<span class="r-in"><span>                                  kernel.func <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># display similarities between kernels</span></span></span>
+<span class="r-in"><span><span class="fu">cim.kernel</span><span class="op">(</span>phychem <span class="op">=</span> <span class="va">phychem.kernel</span>,</span></span>
+<span class="r-in"><span>           pro.phylo <span class="op">=</span> <span class="va">pro.phylo.kernel</span>,</span></span>
+<span class="r-in"><span>           pro.NOGs <span class="op">=</span> <span class="va">pro.NOGs.kernel</span>, </span></span>
+<span class="r-in"><span>           method <span class="op">=</span> <span class="st">"square"</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="cim.kernel-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
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+
+  
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+  
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+  </body></html>
+
diff --git a/docs/reference/combine.kernels.html b/docs/reference/combine.kernels.html
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@@ -0,0 +1,190 @@
+<!DOCTYPE html>
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Combine multiple kernels into a meta-kernel</h1>
+    
+    <div class="hidden name"><code>combine.kernels.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Compute multiple kernels into a single meta-kernel</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">combine.kernels</span><span class="op">(</span></span>
+<span>  <span class="va">...</span>,</span>
+<span>  scale <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"full-UMKL"</span>, <span class="st">"STATIS-UMKL"</span>, <span class="st">"sparse-UMKL"</span><span class="op">)</span>,</span>
+<span>  knn <span class="op">=</span> <span class="fl">5</span>,</span>
+<span>  rho <span class="op">=</span> <span class="fl">20</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>...</dt>
+<dd><p>list of kernels (called 'blocks') computed on different datasets 
+and measured on the same samples.</p></dd>
+
+
+<dt>scale</dt>
+<dd><p>boleean. If <code>scale = TRUE</code>, each block is standardized to 
+zero mean and unit variance and cosine normalization is performed on the 
+kernel. Default: <code>TRUE</code>.</p></dd>
+
+
+<dt>method</dt>
+<dd><p>character. Which method should be used to compute the 
+meta-kernel. Default: <code>"full-UMKL"</code>.</p></dd>
+
+
+<dt>knn</dt>
+<dd><p>integer. If <code>method = "sparse-UMKL"</code> or
+<code>method = "full-UMKL"</code>, number of neighbors used to get a proxy of the 
+local topology of the datasets from each kernel. Default: <code>5</code>.</p></dd>
+
+
+<dt>rho</dt>
+<dd><p>integer. Parameters for the augmented Lagrangian method. Default: 
+<code>20</code>.</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p><code>combine.kernels</code> returns an object of classes <code>"kernel"</code></p>
+ 
+
+<p>and <code>"metaKernel"</code>, a list that contains the following components:</p>
+<dl><dt>kernel</dt>
+<dd><p>: the computed meta-kernel matrix;</p></dd>
+
+  <dt>X</dt>
+<dd><p>: the dataset from which the kernel has been computed, as given by
+  the function <code><a href="compute.kernel.html">compute.kernel</a></code>. Can be <code>NULL</code> if a kernel
+  matrix was passed to this function;</p></dd>
+
+  <dt>weights</dt>
+<dd><p>: a vector containing the weights used to combine the 
+  kernels.</p></dd>
+
+</dl></div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>The arguments <code>method</code> allows to specify the Unsupervised Multiple
+Kernel Learning (UMKL) method to use:</p><ul><li><p><code>"STATIS-UMKL"</code>: combines input kernels into the best 
+  consensus of all kernels;</p></li>
+<li><p><code>"full-UMKL"</code>: computes a kernel that minimizes the distortion 
+  between the meta-kernel and the k-NN graphs obtained from all input 
+  kernels;</p></li>
+<li><p><code>"sparse-UMKL"</code>: a sparse variant of the <code>"full-UMKL"</code> 
+  approach.</p></li>
+</ul></div>
+    <div id="references">
+    <h2>References</h2>
+    <p>Mariette J. and Villa-Vialaneix N. (2018). Unsupervised multiple 
+kernel learning for heterogeneous data integration . <em>Bioinformatics</em>, 
+<b>34</b>(6), 1009-1015. DOI: <a href="https://doi.org/10.1093/bioinformatics/btx682" class="external-link">doi:10.1093/bioinformatics/btx682</a>
+.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code><a href="compute.kernel.html">compute.kernel</a></code>, <code><a href="kernel.pca.html">kernel.pca</a></code></p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># compute one kernel per dataset</span></span></span>
+<span class="r-in"><span><span class="va">phychem.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span>, kernel.func <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">pro.phylo.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.phylo</span>, kernel.func <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">pro.NOGs.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.NOGs</span>, kernel.func <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># compute the meta kernel</span></span></span>
+<span class="r-in"><span><span class="va">meta.kernel</span> <span class="op">&lt;-</span> <span class="fu">combine.kernels</span><span class="op">(</span>phychem <span class="op">=</span> <span class="va">phychem.kernel</span>,</span></span>
+<span class="r-in"><span>                               pro.phylo <span class="op">=</span> <span class="va">pro.phylo.kernel</span>,</span></span>
+<span class="r-in"><span>                               pro.NOGs <span class="op">=</span> <span class="va">pro.NOGs.kernel</span>, </span></span>
+<span class="r-in"><span>                               method <span class="op">=</span> <span class="st">"full-UMKL"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/compute.kernel.html b/docs/reference/compute.kernel.html
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+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Compute a kernel — compute.kernel • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Compute a kernel — compute.kernel"><meta property="og:description" content="Compute a kernel from a given data matrix."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+    </li>
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Compute a kernel</h1>
+    
+    <div class="hidden name"><code>compute.kernel.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Compute a kernel from a given data matrix.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">compute.kernel</span><span class="op">(</span><span class="va">X</span>, kernel.func <span class="op">=</span> <span class="st">"linear"</span>, <span class="va">...</span>, test.pos.semidef <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>X</dt>
+<dd><p>a numeric matrix (or data frame) used to compute the kernel. 
+<code>NA</code>s not allowed.</p></dd>
+
+
+<dt>kernel.func</dt>
+<dd><p>the kernel function to use. This parameter can be set to 
+any user defined kernel function. Widely used kernel functions are 
+pre-implemented, that can be used by setting <code>kernel.func</code> to one of the
+ following strings: <code>"kidentity"</code>, <code>"abundance"</code>, <code>"linear"</code>, 
+<code>"gaussian.radial.basis"</code>, <code>"poisson"</code> or <code>"phylogenetic"</code>. 
+Default: <code>"linear"</code>.</p></dd>
+
+
+<dt>...</dt>
+<dd><p>the kernel function arguments. Valid parameters for 
+pre-implemented kernels are:</p><ul><li><p><code>phylogenetic.tree</code> (<code>"phylogenetic"</code>): an instance of 
+    phylo-class that contains a phylogenetic tree (required).</p></li>
+<li><p><code>scale</code> (<code>"linear"</code> or <code>"gaussian.radial.basis"</code>): 
+      logical. Should the variables be scaled to unit variance prior the 
+      kernel computation? Default: <code>TRUE</code>.</p></li>
+<li><p><code>sigma</code> (<code>"gaussian.radial.basis"</code>): double. The inverse 
+    kernel width used by <code>"gaussian.radial.basis"</code>.</p></li>
+<li><p><code>method</code> (<code>"phylogenetic"</code> or <code>"abundance"</code>): 
+    character. Can be <code>"unifrac"</code> or <code>"wunifrac"</code> for 
+    <code>"phylogenetic"</code>. Which dissimilarity to use for <code>"abundance"</code>:
+    one of <code>"bray"</code>, <code>"euclidean"</code>, <code>"canberra"</code>, 
+    <code>"manhattan"</code>, <code>"kulczynski"</code>, <code>"jaccard"</code>, 
+    <code>"gower"</code>, <code>"altGower"</code>, <code>"morisita"</code>, <code>"horn"</code>, 
+    <code>"mountford"</code>, <code>"raup"</code>, <code>"binomial"</code>, <code>"chao"</code> and 
+    <code>"cao"</code>.</p></li>
+<li><p><code>normalization</code> (<code>"poisson"</code>): character. Can be 
+    <code>"deseq"</code> (more robust), <code>"mle"</code> (less robust) or 
+    <code>"quantile"</code>.</p></li>
+</ul></dd>
+
+
+<dt>test.pos.semidef</dt>
+<dd><p>boleean. If <code>test.pos.semidef = TRUE</code>, the 
+positive semidefiniteness of the resulting matrix is checked.</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p><code>compute.kernel</code> returns an object of classes <code>"kernel"</code>, a
+list that contains the following components:</p>
+<dl><dt>kernel</dt>
+<dd><p>: the computed kernel matrix.</p></dd>
+
+<dt>X</dt>
+<dd><p>: the original dataset. If <code>"kidentity"</code>, <code>X</code> is set to 
+<code>NULL</code>.</p></dd>
+
+<dt>kernel.func</dt>
+<dd><p>: the kernel function used.</p></dd>
+
+<dt>kernel.args</dt>
+<dd><p>: the arguments used to compute the kernel.</p></dd>
+
+</dl></div>
+    <div id="references">
+    <h2>References</h2>
+    <p>Lozupone C. and Knight R. (2005). UniFrac: a new phylogenetic 
+method for comparing microbial communities. <em>Applied and Environmental 
+Microbiology</em>, <b>71</b>(12), 8228-8235.</p>
+<p>Lozupone C., Hamady M., Kelley S.T. and Knight R. (2007). Quantitative and 
+qualitative beta diversity measures lead to different insights into factors 
+that structure microbial communities. <em>Applied and Environmental 
+Microbiology</em>, <b>73</b>(5), 1576-1585.</p>
+<p>Witten D. (2011). Classification and clustering of sequencing data using a 
+Poisson model. <em>Annals of Applied Statistics</em>, <b>5</b>(4), 2493-2518.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code><a href="combine.kernels.html">combine.kernels</a></code>, <code><a href="kernel.pca.html">kernel.pca</a></code></p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">pro.NOGs.kernel</span> <span class="op">&lt;-</span> <span class="fu">compute.kernel</span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">pro.NOGs</span>, </span></span>
+<span class="r-in"><span>                                  kernel.func <span class="op">=</span> <span class="st">"abundance"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
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+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
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+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
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+
diff --git a/docs/reference/index.html b/docs/reference/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..fd29ea99e95f1ba93bdba6cc598386fa7d64eab5
--- /dev/null
+++ b/docs/reference/index.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Function reference • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+</li>
+<li class="dropdown">
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+    Articles
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+  </a>
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+      <a href="../articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="../articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
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+
+      
+
+      </header><div class="row">
+  <div class="contents col-md-9">
+    <div class="page-header">
+      <h1>Reference</h1>
+    </div>
+
+    <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
+          <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" aria-hidden="true"></a></h2>
+          <p class="section-desc"></p>
+        </th>
+      </tr></tbody><tbody><tr><td>
+          <p><code><a href="TARAoceans.html">TARAoceans</a></code> </p>
+        </td>
+        <td><p>TARA ocean microbiome data</p></td>
+      </tr><tr><td>
+          <p><code><a href="center.scale.html">center.scale()</a></code> </p>
+        </td>
+        <td><p>Center and scale</p></td>
+      </tr><tr><td>
+          <p><code><a href="cim.kernel.html">cim.kernel()</a></code> </p>
+        </td>
+        <td><p>Compute and display similarities between multiple kernels</p></td>
+      </tr><tr><td>
+          <p><code><a href="combine.kernels.html">combine.kernels()</a></code> </p>
+        </td>
+        <td><p>Combine multiple kernels into a meta-kernel</p></td>
+      </tr><tr><td>
+          <p><code><a href="compute.kernel.html">compute.kernel()</a></code> </p>
+        </td>
+        <td><p>Compute a kernel</p></td>
+      </tr><tr><td>
+          <p><code><a href="kernel.pca.html">kernel.pca()</a></code> </p>
+        </td>
+        <td><p>Kernel Principal Components Analysis</p></td>
+      </tr><tr><td>
+          <p><code><a href="kernel.pca.permute.html">kernel.pca.permute()</a></code> </p>
+        </td>
+        <td><p>Assess variable importance</p></td>
+      </tr><tr><td>
+          <p><code><a href="mixKernel.users.guide.html">mixKernel.users.guide()</a></code> </p>
+        </td>
+        <td><p>View mixKernel User's Guide</p></td>
+      </tr><tr><td>
+          <p><code><a href="plotVar.kernel.pca.html">plotVar.kernel.pca()</a></code> </p>
+        </td>
+        <td><p>Plot importance of variables in kernel PCA</p></td>
+      </tr><tr><td>
+          <p><code><a href="select.features.html">select(<i>&lt;features&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Select important features</p></td>
+      </tr></tbody></table></div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
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diff --git a/docs/reference/kernel.pca.html b/docs/reference/kernel.pca.html
new file mode 100644
index 0000000000000000000000000000000000000000..9c9f1748e85d3aab279ebdbbcb0d13330e4c51eb
--- /dev/null
+++ b/docs/reference/kernel.pca.html
@@ -0,0 +1,155 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Kernel Principal Components Analysis — kernel.pca • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Kernel Principal Components Analysis — kernel.pca"><meta property="og:description" content="Performs a kernel PCA."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+  <a href="../reference/index.html">Reference</a>
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+      <a href="../articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
+    </li>
+    <li>
+      <a href="../articles/mixKernelUsersGuide.html">Data Integration using Unsupervised Multiple Kernel Learning</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Kernel Principal Components Analysis</h1>
+    
+    <div class="hidden name"><code>kernel.pca.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Performs a kernel PCA.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">kernel.pca</span><span class="op">(</span><span class="va">K</span>, ncomp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">K</span><span class="op">$</span><span class="va">kernel</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>K</dt>
+<dd><p>a kernel object obtained using either <code>compute.kernel</code> or
+<code>combine.kernels</code>.</p></dd>
+
+
+<dt>ncomp</dt>
+<dd><p>integer. Indicates the number of components to return..</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p><code>kernel.pca</code> returns an object of classes <code>"kernel.pca"</code></p>
+ 
+
+<p>and <code>"pca"</code>, which is a list containing the following entries:</p>
+<dl><dt>ncomp</dt>
+<dd><p>: the number of principal components;</p></dd>
+
+  <dt>X</dt>
+<dd><p>: the input kernel matrix;</p></dd>
+ 
+  <dt>kernel</dt>
+<dd><p>: the input kernel object provided by the user;</p></dd>
+
+  <dt>sdev</dt>
+<dd><p>: the singular values (square root of the eigenvalues);</p></dd>
+ 
+  <dt>rotation</dt>
+<dd><p>: the matrix of variable loadings (<em>i.e.</em>, a matrix 
+  whose columns contain the eigenvectors);</p></dd>
+
+  <dt>loadings</dt>
+<dd><p>: same as 'rotation' to keep the mixOmics spirit;</p></dd>
+
+  <dt>x</dt>
+<dd><p>: same as 'rotation' to keep the mixOmics spirit;</p></dd>
+
+</dl></div>
+    <div id="references">
+    <h2>References</h2>
+    <p>Scholkopf B., Smola A. and Muller K.R. (1998) Nonlinear component 
+analysis as a kernel eigenvalue problem. <em>Neural Computation</em>, 
+<b>10</b>, 1299-1319.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code><a href="compute.kernel.html">compute.kernel</a></code>, <code><a href="combine.kernels.html">combine.kernels</a></code></p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">phychem.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span>, kernel.func <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">kernel.pca.result</span> <span class="op">&lt;-</span> <span class="fu">kernel.pca</span><span class="op">(</span><span class="va">phychem.kernel</span>, ncomp <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/kernel.pca.permute.html b/docs/reference/kernel.pca.permute.html
new file mode 100644
index 0000000000000000000000000000000000000000..2a338811f913d2273017d7b0a1f2c8cfe19d77bf
--- /dev/null
+++ b/docs/reference/kernel.pca.permute.html
@@ -0,0 +1,168 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Assess variable importance — kernel.pca.permute • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Assess variable importance — kernel.pca.permute"><meta property="og:description" content="Assess importance of variables on a given PC component by computing the 
+Crone-Crosby distance between original sample positions and sample positions 
+obtained by a random permutation of the variables."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+      
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Assess variable importance</h1>
+    
+    <div class="hidden name"><code>kernel.pca.permute.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Assess importance of variables on a given PC component by computing the 
+Crone-Crosby distance between original sample positions and sample positions 
+obtained by a random permutation of the variables.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">kernel.pca.permute</span><span class="op">(</span><span class="va">kpca.result</span>, ncomp <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span>, directory <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>kpca.result</dt>
+<dd><p>a kernel.pca object returned by the
+<code><a href="kernel.pca.html">kernel.pca</a></code> function.</p></dd>
+
+
+<dt>ncomp</dt>
+<dd><p>integer. Number of KPCA components used to compute the 
+importance. Default: <code>1</code>.</p></dd>
+
+
+<dt>...</dt>
+<dd><p>list of character vectors. The parameter name must be the kernel 
+name to be considered for permutation of variables. Provided vectors length 
+has to be equal to the number of variables of the input dataset. A kernel is 
+performed on each unique variables values. Crone-Crosby distances are 
+computed on each KPCA performed on resulted kernels or meta-kernels and can 
+be displayed using the <code><a href="plotVar.kernel.pca.html">plotVar.kernel.pca</a></code>.</p></dd>
+
+
+<dt>directory</dt>
+<dd><p>character. To limit computational burden, this argument 
+allows to store / read temporary computed kernels.</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p><code>kernel.pca.permute</code> returns a copy of the input 
+<code>kpca.result</code> results and add values in the three entries: 
+<code>cc.distances</code>, <code>cc.variables</code> and <code>cc.blocks</code>.</p>
+    </div>
+    <div id="details">
+    <h2>Details</h2>
+    <p><code>plotVar.kernel.pca</code> produces a barplot for each block. The variables 
+for which the importance has been computed with 
+<code>kernel.pca.permute</code> are displayed. The representation is limited 
+to the <code>ndisplay</code> most important variables.</p>
+    </div>
+    <div id="references">
+    <h2>References</h2>
+    <p>Mariette J. and Villa-Vialaneix N. (2018). Unsupervised multiple 
+kernel learning for heterogeneous data integration. <em>Bioinformatics</em>, 
+<b>34</b>(6), 1009-1015. DOI: <a href="https://doi.org/10.1093/bioinformatics/btx682" class="external-link">doi:10.1093/bioinformatics/btx682</a></p>
+<p>Crone L. and Crosby D. (1995). Statistical applications of a metric on 
+subspaces to satellite meteorology. <em>Technometrics</em>, <b>37</b>(3), 
+324-328.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code><a href="compute.kernel.html">compute.kernel</a></code>, <code><a href="kernel.pca.html">kernel.pca</a></code></p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># compute one kernel for the psychem dataset</span></span></span>
+<span class="r-in"><span><span class="va">phychem.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span>, kernel.func <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># perform a KPCA</span></span></span>
+<span class="r-in"><span><span class="va">kernel.pca.result</span> <span class="op">&lt;-</span> <span class="fu"><a href="kernel.pca.html">kernel.pca</a></span><span class="op">(</span><span class="va">phychem.kernel</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># compute importance for all variables in this kernel</span></span></span>
+<span class="r-in"><span><span class="va">kernel.pca.result</span> <span class="op">&lt;-</span> <span class="fu">kernel.pca.permute</span><span class="op">(</span><span class="va">kernel.pca.result</span>, </span></span>
+<span class="r-in"><span>                                        phychem <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
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+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+
diff --git a/docs/reference/mixKernel.users.guide.html b/docs/reference/mixKernel.users.guide.html
new file mode 100644
index 0000000000000000000000000000000000000000..dda2b5943ffd051723f5f16a3d1e6147e0d84755
--- /dev/null
+++ b/docs/reference/mixKernel.users.guide.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>View mixKernel User's Guide — mixKernel.users.guide • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="View mixKernel User's Guide — mixKernel.users.guide"><meta property="og:description" content="Find the location of the mixKernel User's Guide and optionnaly opens it"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
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+    </li>
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+    <div class="page-header">
+    <h1>View mixKernel User's Guide</h1>
+    
+    <div class="hidden name"><code>mixKernel.users.guide.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Find the location of the mixKernel User's Guide and optionnaly opens it</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mixKernel.users.guide</span><span class="op">(</span>html <span class="op">=</span> <span class="cn">TRUE</span>, view <span class="op">=</span> <span class="va">html</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>html</dt>
+<dd><p>logical. Should the document returned by the function be the
+compiled PDF or the Rmd source. Default to <code>TRUE</code></p></dd>
+
+
+<dt>view</dt>
+<dd><p>logical. Should the document be opened using the default HTML
+viewer? Default to <code>html</code>. It has no effect if <code>html = FALSE</code></p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>Character string giving the file location. If <code>html = TRUE</code> and
+<code>view = TRUE</code>, the HTML document reader is started and the User's Guide
+is opened in it.</p>
+    </div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>If the operating system is not Windows, then the HTML viewer used is that
+given by <code>Sys.getenv("R_BROWSER")</code>. The HTML viewer can be changed using
+<code>Sys.setenv(R_BROWSER = )</code>.</p>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">mixKernel.users.guide</span><span class="op">(</span>view <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
+<span class="r-in"><span><span class="fu">mixKernel.users.guide</span><span class="op">(</span>html <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">mixKernel.users.guide</span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
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+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/plotVar.kernel.pca.html b/docs/reference/plotVar.kernel.pca.html
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@@ -0,0 +1,157 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Plot importance of variables in kernel PCA — plotVar.kernel.pca • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Plot importance of variables in kernel PCA — plotVar.kernel.pca"><meta property="og:description" content="Provides a representation of variable importance in kernel PCA."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+      <a href="../articles/a-mixKernelInstallation.html">Installation instruction for mixKernel</a>
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+      
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Plot importance of variables in kernel PCA</h1>
+    
+    <div class="hidden name"><code>plotVar.kernel.pca.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Provides a representation of variable importance in kernel PCA.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plotVar.kernel.pca</span><span class="op">(</span></span>
+<span>  <span class="va">object</span>,</span>
+<span>  blocks <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">cc.blocks</span><span class="op">)</span>,</span>
+<span>  ndisplay <span class="op">=</span> <span class="fl">5</span>,</span>
+<span>  ncol <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>object</dt>
+<dd><p>: a kernel.pca object returned by <code><a href="kernel.pca.html">kernel.pca</a></code>.</p></dd>
+
+
+<dt>blocks</dt>
+<dd><p>a numerical vector indicating the block variables to display.</p></dd>
+
+
+<dt>ndisplay</dt>
+<dd><p>integer. The number of important variables per blocks shown in 
+the representation. Default: <code>5</code>.</p></dd>
+
+
+<dt>ncol</dt>
+<dd><p>integer. Each block of variables is displayed in a separate 
+subfigure. <code>ncol</code> sets the number of columns for the global figure. 
+Default: <code>2</code>.</p></dd>
+
+
+<dt>...</dt>
+<dd><p>external arguments.</p></dd>
+
+</dl></div>
+    <div id="details">
+    <h2>Details</h2>
+    <p><code>plotVar.kernel.pca</code> produces a barplot for each block. The variables for which the 
+importance has been computed with <code><a href="kernel.pca.permute.html">kernel.pca.permute</a></code> are 
+displayed. The representation is limited to the <code>ndisplay</code> most important 
+variables.</p>
+    </div>
+    <div id="references">
+    <h2>References</h2>
+    <p>Crone L. and Crosby D. (1995). Statistical applications of a metric on subspaces
+to satellite meteorology. <em>Technometrics</em>, <b>37</b>(3), 324-328.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code><a href="kernel.pca.html">kernel.pca</a></code>, <code><a href="kernel.pca.permute.html">kernel.pca.permute</a></code></p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># compute one kernel for the psychem dataset</span></span></span>
+<span class="r-in"><span><span class="va">phychem.kernel</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute.kernel.html">compute.kernel</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span>, kernel.func <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># perform a KPCA</span></span></span>
+<span class="r-in"><span><span class="va">kernel.pca.result</span> <span class="op">&lt;-</span> <span class="fu"><a href="kernel.pca.html">kernel.pca</a></span><span class="op">(</span><span class="va">phychem.kernel</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># compute importance for all variables in this kernel</span></span></span>
+<span class="r-in"><span><span class="va">kernel.pca.result</span> <span class="op">&lt;-</span> <span class="fu"><a href="kernel.pca.permute.html">kernel.pca.permute</a></span><span class="op">(</span><span class="va">kernel.pca.result</span>, phychem <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">TARAoceans</span><span class="op">$</span><span class="va">phychem</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">plotVar.kernel.pca</span><span class="op">(</span><span class="va">kernel.pca.result</span>, ndisplay <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/select.features.html b/docs/reference/select.features.html
new file mode 100644
index 0000000000000000000000000000000000000000..94a928210c6880613be2f50a840ad4e0b17616a5
--- /dev/null
+++ b/docs/reference/select.features.html
@@ -0,0 +1,227 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Select important features — select.features • mixKernel</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Select important features — select.features"><meta property="og:description" content="Select features using supervised or unsupervised kernel method. A 
+supervised feature selection method is performed if Y is provided."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+    </li>
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Select important features</h1>
+    
+    <div class="hidden name"><code>select.features.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Select features using supervised or unsupervised kernel method. A 
+supervised feature selection method is performed if <code>Y</code> is provided.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for features</span></span>
+<span><span class="fu">select</span><span class="op">(</span></span>
+<span>  <span class="va">X</span>,</span>
+<span>  Y <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  kx.func <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"linear"</span>, <span class="st">"gaussian.radial.basis"</span>, <span class="st">"bray"</span><span class="op">)</span>,</span>
+<span>  ky.func <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"linear"</span>, <span class="st">"gaussian.radial.basis"</span><span class="op">)</span>,</span>
+<span>  keepX <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"kernel"</span>, <span class="st">"kpca"</span>, <span class="st">"graph"</span><span class="op">)</span>,</span>
+<span>  lambda <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  n_components <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>  Lg <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  mu <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  max_iter <span class="op">=</span> <span class="fl">100</span>,</span>
+<span>  nstep <span class="op">=</span> <span class="fl">50</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>X</dt>
+<dd><p>a numeric matrix (or data frame) used to select variables. 
+<code>NA</code>s not allowed.</p></dd>
+
+
+<dt>Y</dt>
+<dd><p>a numeric matrix (or data frame) used to select variables. 
+<code>NA</code>s not allowed.</p></dd>
+
+
+<dt>kx.func</dt>
+<dd><p>the kernel function name to use on <code>X</code>. Widely used 
+kernel functions are pre-implemented, and can be directly used by setting 
+<code>kx.func</code> to one of the following values: <code>"linear"</code>, 
+<code>"gaussian.radial.basis"</code> or <code>"bray"</code>. Default: <code>"linear"</code>. If 
+<code>Y</code> is provided, the kernel <code>"bray"</code> is not allowed.</p></dd>
+
+
+<dt>ky.func</dt>
+<dd><p>the kernel function name to use on <code>Y</code>. Available 
+kernels are: <code>"linear"</code>, and <code>"gaussian.radial.basis"</code>. Default: 
+<code>"linear"</code>. This value is ignored when <code>Y</code> is not provided.</p></dd>
+
+
+<dt>keepX</dt>
+<dd><p>the number of variables to select.</p></dd>
+
+
+<dt>method</dt>
+<dd><p>the method to use. Either an unsupervised variable selection
+method (<code>"kernel"</code>), a kernel PCA oriented variable selection method 
+(<code>"kpca"</code>) or a structure driven variable selection selection 
+(<code>"graph"</code>). Default: <code>"kernel"</code>.</p></dd>
+
+
+<dt>lambda</dt>
+<dd><p>the penalization parameter that controls the trade-off between 
+the minimization of the distorsion and the sparsity of the solution 
+parameter.</p></dd>
+
+
+<dt>n_components</dt>
+<dd><p>how many principal components should be used with method
+<code>"kpca"</code>. Required with method <code>"kpca"</code>. Default: <code>2</code>.</p></dd>
+
+
+<dt>Lg</dt>
+<dd><p>the Laplacian matrix of the graph representing relations between 
+the input dataset variables. Required with method <code>"graph"</code>.</p></dd>
+
+
+<dt>mu</dt>
+<dd><p>the penalization parameter that controls the trade-off between the
+the distorsion and the influence of the graph. Default: <code>1</code>.</p></dd>
+
+
+<dt>max_iter</dt>
+<dd><p>the maximum number of iterations. Default: <code>100</code>.</p></dd>
+
+
+<dt>nstep</dt>
+<dd><p>the number of values used for the regularization path. Default: 
+<code>50</code>.</p></dd>
+
+
+<dt>...</dt>
+<dd><p>the kernel function arguments. In particular, 
+<code>sigma</code>(<code>"gaussian.radial.basis"</code>): double. The inverse kernel 
+width used by <code>"gaussian.radial.basis"</code>.</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p><code>ukfs</code> returns a vector of sorted selected features indexes.</p>
+    </div>
+    <div id="references">
+    <h2>References</h2>
+    <p>Brouard C., Mariette J., Flamary R. and Vialaneix N. (2022). 
+Feature selection for kernel methods in systems biology. <em>NAR Genomics
+and Bioinformatics</em>, <b>4</b>(1), lqac014. DOI: <a href="https://doi.org/10.1093/nargab/lqac014" class="external-link">doi:10.1093/nargab/lqac014</a>
+.</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p><code><a href="compute.kernel.html">compute.kernel</a></code></p></div>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Celine Brouard &lt;celine.brouard@inrae.fr&gt;
+Jerome Mariette &lt;jerome.mariette@inrae.fr&gt;
+Nathalie Vialaneix &lt;nathalie.vialaneix@inrae.fr&gt;</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## These examples require the installation of python modules</span></span></span>
+<span class="r-in"><span><span class="co">## See installation instruction at: http://mixkernel.clementine.wf</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"Koren.16S"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span> <span class="va">sf.res</span> <span class="op">&lt;-</span> <span class="fu">select.features</span><span class="op">(</span><span class="va">Koren.16S</span><span class="op">$</span><span class="va">data.raw</span>, kx.func <span class="op">=</span> <span class="st">"bray"</span>, lambda <span class="op">=</span> <span class="fl">1</span>,</span></span>
+<span class="r-in"><span>                           keepX <span class="op">=</span> <span class="fl">40</span>, nstep <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">Koren.16S</span><span class="op">$</span><span class="va">data.raw</span><span class="op">)</span><span class="op">[</span><span class="va">sf.res</span><span class="op">]</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"nutrimouse"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span> <span class="va">grb.func</span> <span class="op">&lt;-</span> <span class="st">"gaussian.radial.basis"</span></span></span>
+<span class="r-in"><span> <span class="va">genes</span> <span class="op">&lt;-</span> <span class="fu"><a href="center.scale.html">center.scale</a></span><span class="op">(</span><span class="va">nutrimouse</span><span class="op">$</span><span class="va">gene</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">lipids</span> <span class="op">&lt;-</span> <span class="fu"><a href="center.scale.html">center.scale</a></span><span class="op">(</span><span class="va">nutrimouse</span><span class="op">$</span><span class="va">lipid</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">sf.res</span> <span class="op">&lt;-</span> <span class="fu">select.features</span><span class="op">(</span><span class="va">genes</span>, <span class="va">lipids</span>, kx.func <span class="op">=</span> <span class="va">grb.func</span>, </span></span>
+<span class="r-in"><span>                           ky.func <span class="op">=</span> <span class="va">grb.func</span>, keepX <span class="op">=</span> <span class="fl">40</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">nutrimouse</span><span class="op">$</span><span class="va">gene</span><span class="op">)</span><span class="op">[</span><span class="va">sf.res</span><span class="op">]</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Nathalie Vialaneix, Celine Brouard, Remi Flamary, Julien Henry, Jerome Mariette.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a1d660d459c3073abdacf80e9f6919691ab04562
--- /dev/null
+++ b/docs/sitemap.xml
@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
+  <url>
+    <loc>/404.html</loc>
+  </url>
+  <url>
+    <loc>/articles/0-mixKernelInstallation.html</loc>
+  </url>
+  <url>
+    <loc>/articles/a-mixKernelInstallation.html</loc>
+  </url>
+  <url>
+    <loc>/articles/index.html</loc>
+  </url>
+  <url>
+    <loc>/articles/mixKernelUsersGuide.html</loc>
+  </url>
+  <url>
+    <loc>/authors.html</loc>
+  </url>
+  <url>
+    <loc>/index.html</loc>
+  </url>
+  <url>
+    <loc>/news/index.html</loc>
+  </url>
+  <url>
+    <loc>/reference/TARAoceans.html</loc>
+  </url>
+  <url>
+    <loc>/reference/center.scale.html</loc>
+  </url>
+  <url>
+    <loc>/reference/cim.kernel.html</loc>
+  </url>
+  <url>
+    <loc>/reference/combine.kernels.html</loc>
+  </url>
+  <url>
+    <loc>/reference/compute.kernel.html</loc>
+  </url>
+  <url>
+    <loc>/reference/index.html</loc>
+  </url>
+  <url>
+    <loc>/reference/kernel.pca.html</loc>
+  </url>
+  <url>
+    <loc>/reference/kernel.pca.permute.html</loc>
+  </url>
+  <url>
+    <loc>/reference/mixKernel.users.guide.html</loc>
+  </url>
+  <url>
+    <loc>/reference/plotVar.kernel.pca.html</loc>
+  </url>
+  <url>
+    <loc>/reference/select.features.html</loc>
+  </url>
+</urlset>
diff --git a/man/combine.kernels.Rd b/man/combine.kernels.Rd
index ae49b1f16e74fefe45455d24591f5679a22168dc..2417c827c21ef9c46a1598cff245a72cf93610be 100644
--- a/man/combine.kernels.Rd
+++ b/man/combine.kernels.Rd
@@ -31,15 +31,14 @@ local topology of the datasets from each kernel. Default: \code{5}.}
 \code{20}.}
 }
 \value{
-\code{combine.kernels} returns an object of classes \code{"kernel"} and 
-\code{"metaKernel"}, a list that contains the following components: \itemize{
+\code{combine.kernels} returns an object of classes \code{"kernel"} 
+and \code{"metaKernel"}, a list that contains the following components: 
   \item{kernel}{: the computed meta-kernel matrix;}
   \item{X}{: the dataset from which the kernel has been computed, as given by
   the function \code{\link{compute.kernel}}. Can be \code{NULL} if a kernel
   matrix was passed to this function;}
   \item{weights}{: a vector containing the weights used to combine the 
-  kernels.} 
-}
+  kernels.}
 }
 \description{
 Compute multiple kernels into a single meta-kernel
@@ -47,13 +46,14 @@ Compute multiple kernels into a single meta-kernel
 \details{
 The arguments \code{method} allows to specify the Unsupervised Multiple
 Kernel Learning (UMKL) method to use: \itemize{
-  \item{\code{"STATIS-UMKL"}}{: combines input kernels into the best 
-  consensus of all kernels;}
-  \item \code{"full-UMKL"}{: computes a kernel that minimizes the distortion 
+  \item \code{"STATIS-UMKL"}: combines input kernels into the best 
+  consensus of all kernels;
+  \item \code{"full-UMKL"}: computes a kernel that minimizes the distortion 
   between the meta-kernel and the k-NN graphs obtained from all input 
-  kernels;}
-  \item \code{"sparse-UMKL"}{: a sparse variant of the \code{"full-UMKL"} 
-  approach.}}
+  kernels;
+  \item \code{"sparse-UMKL"}: a sparse variant of the \code{"full-UMKL"} 
+  approach.
+}
 }
 \examples{
 data(TARAoceans)
diff --git a/man/compute.kernel.Rd b/man/compute.kernel.Rd
index 57f947a56aaf3c9d4137ba885ea272fd2a6ed5e2..b3350bccb3df9031276c6c8b3c7fa76e926d6dce 100644
--- a/man/compute.kernel.Rd
+++ b/man/compute.kernel.Rd
@@ -18,8 +18,7 @@ pre-implemented, that can be used by setting \code{kernel.func} to one of the
 Default: \code{"linear"}.}
 
 \item{...}{the kernel function arguments. Valid parameters for 
-pre-implemented kernels are: 
-  \itemize{
+pre-implemented kernels are: \itemize{
     \item \code{phylogenetic.tree} (\code{"phylogenetic"}): an instance of 
     phylo-class that contains a phylogenetic tree (required).
     \item \code{scale} (\code{"linear"} or \code{"gaussian.radial.basis"}): 
@@ -37,7 +36,8 @@ pre-implemented kernels are:
     \code{"cao"}.
     \item \code{normalization} (\code{"poisson"}): character. Can be 
     \code{"deseq"} (more robust), \code{"mle"} (less robust) or 
-    \code{"quantile"}.}}
+    \code{"quantile"}.
+}}
 
 \item{test.pos.semidef}{boleean. If \code{test.pos.semidef = TRUE}, the 
 positive semidefiniteness of the resulting matrix is checked.}
diff --git a/man/kernel.pca.Rd b/man/kernel.pca.Rd
index 11a99f1dc32d30c26bdb881c773045b05385a4a7..4e57d198cd7662c6cd502e8af8154912a45ad4c3 100644
--- a/man/kernel.pca.Rd
+++ b/man/kernel.pca.Rd
@@ -14,7 +14,7 @@ kernel.pca(K, ncomp = nrow(K$kernel))
 }
 \value{
 \code{kernel.pca} returns an object of classes \code{"kernel.pca"} 
-and \code{"pca"}, which is a list containing the following entries: \itemize{
+and \code{"pca"}, which is a list containing the following entries: 
   \item{ncomp}{: the number of principal components;}
   \item{X}{: the input kernel matrix;} 
   \item{kernel}{: the input kernel object provided by the user;}
@@ -24,7 +24,6 @@ and \code{"pca"}, which is a list containing the following entries: \itemize{
   \item{loadings}{: same as 'rotation' to keep the mixOmics spirit;}
   \item{x}{: same as 'rotation' to keep the mixOmics spirit;}
 }
-}
 \description{
 Performs a kernel PCA.
 }
diff --git a/vignettes/a-mixKernelInstallation.Rmd b/vignettes/a-mixKernelInstallation.Rmd
index a59dfc6266ffef3baa2d2c698a110e2735c15c0a..0c409297290f9a610fdeb158e0f5ae37c5bf979d 100644
--- a/vignettes/a-mixKernelInstallation.Rmd
+++ b/vignettes/a-mixKernelInstallation.Rmd
@@ -8,13 +8,12 @@ output:
     code_folding: show
     highlight: haddock
     df_print: kable
+vignette: >
+  %\VignetteIndexEntry{Installation instruction}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
-<!--
-%\VignetteEngine{knitr}
-%\VignetteIndexEntry{Installation instruction}
-%\VignettePackage{mixKernel}
--->
 
 This vignette provide installation for `mixKernel` instructions. 
 
diff --git a/vignettes/mixKernelUsersGuide.Rmd b/vignettes/mixKernelUsersGuide.Rmd
index ad3bcb28374631116961204534e496ead26e3849..b8e817267838e533470bc2aa4b4a6d5c0e54d7c1 100644
--- a/vignettes/mixKernelUsersGuide.Rmd
+++ b/vignettes/mixKernelUsersGuide.Rmd
@@ -8,14 +8,12 @@ output:
     code_folding: show
     highlight: haddock
     df_print: kable
+vignette: >
+  %\VignetteIndexEntry{Integrative exploratory analysis with mixKernel}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
-<!--
-%\VignetteEngine{knitr}
-%\VignetteIndexEntry{Integrative exploratory analysis with mixKernel}
-%\VignettePackage{mixKernel}
--->
-
 # Introduction
 
 The TARA Oceans expedition facilitated the study of plankton communities by