diff --git a/.gitignore b/.gitignore
index 00b624d59f9538d50c66c609640c7b2f807774cc..8f2e298630a72c318ffa5a6b35b80ac623fe1263 100644
--- a/.gitignore
+++ b/.gitignore
@@ -56,3 +56,5 @@ scaterPlot.png
 # videos are on youtube
 *.mp4
 
+# specific files
+vignettes/pkdown/scran.grunPancreas.RData
diff --git a/DESCRIPTION b/DESCRIPTION
index d9b9ea755d03d9239683a1328f0da3257cd1c905..6ce7e603c5397feb48f4d60622ce2d4e2d526e1c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SCHNAPPs
 Type: Package
 Title: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
-Version: 1.4.59
+Version: 1.4.60
 Authors@R: c(person("Bernd", "Jagla", role = c("aut", "cre"), email = "bernd.jagla@pasteur.fr", comment = c(ORCID = "0000-0002-7696-0484")))
 Maintainer: Bernd Jagla <bernd.jagla@pasteur.fr>
 Description: Single Cell sHiny APPlication (SCHNAPPs) is a R/Shiny based application to interact, manipulate, explore, and analyze single cell RNA-seq experiments, including MARS-seq and others.
diff --git a/R/schnapps-Lite.R b/R/schnapps-Lite.R
index 7ee4ca5bdfb84f5e9b8e12cc2428e695c6c583b2..8e4eb84ce4874347ae113dc12460f2765c7cb8af 100644
--- a/R/schnapps-Lite.R
+++ b/R/schnapps-Lite.R
@@ -130,65 +130,3 @@ schnappsLite <- function(data="RdataFile",
 # schnapps(localContributionDir = "~/Rstudio/__shHubgit/bjContributions",  defaultValueSingleGene = "cd52", defaultValueMultiGenes = "S100A4, CD52, S100A9, S100A8,")
 
 
-
-#' Example data for schnapps app
-#'
-#' A dataset containing the prices and other attributes of almost 54,000
-#' diamonds. The variables are as follows:
-#'
-#' * `scExLite`: singlecellExperiment object
-#'
-#' @format A data frame with 53940 rows and 10 variables
-#' @source <http://www.diamondse.info/>
-# "scExLite"
-
-#' * `ccol` : color definitions
-#' @format a vector with colours used for clusters
-"ccol"
-
-#' 
-#' * `scol` : color definitions for samples
-#' @format a vector of colour values for samples
-"scol"
-
-#' 
-#' * `pca` : pca results, Eigenvalues and vectors.
-#' @format List with "x", "var_pcs", "rotation"
-"pca"
-
-
-#' 
-#' * `geneCount` : number of genes per cell.
-#' @format List with "x", "var_pcs", "rotation"
-"geneCount"       
-
-
-#' 
-#' * `pca` : pca results, Eigenvalues and vectors.
-#' @format List with "x", "var_pcs", "rotation"
-"umiCount"        
-
-
-#' 
-#' * `beforeFilterPrj` : number of reads that got filtered out
-#' @format List with "x", "var_pcs", "rotation"
-"beforeFilterPrj" 
-
-#' 
-#' * `tsne` : tsne projection.
-#' @format List with "x", "var_pcs", "rotation"
-"tsne"            
-
-
-
-#' 
-#' * `dbCluster` : used clustering
-#' @format List with "x", "var_pcs", "rotation"
-"dbCluster"       
-
-
-
-#' 
-#' * `umapReact` : umap projections
-#' @format List with "x", "var_pcs", "rotation"
-"umapReact" 
diff --git a/docs/404.html b/docs/404.html
index 340665cfd0aa9e78c2198bac6a0955218b8c1fe5..a11755c886bf029ac570b797c2f5586e450e85bb 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -79,7 +79,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -110,6 +110,9 @@
     <li>
       <a href="articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
index afacc79e6b314a4252c455f9b2eb23195a979681..3f3d1fb5bd7c916c94268dbb9873f37b762d5f65 100644
--- a/docs/CONTRIBUTING.html
+++ b/docs/CONTRIBUTING.html
@@ -79,7 +79,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -110,6 +110,9 @@
     <li>
       <a href="articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/articles/Readme.html b/docs/articles/Readme.html
index abc822afed8da98853b232dda216c3e74cccd26b..4adea7d50a3a867c227d13e66f83a95bae85b2a8 100644
--- a/docs/articles/Readme.html
+++ b/docs/articles/Readme.html
@@ -38,7 +38,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -69,6 +69,9 @@
     <li>
       <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 2829dbefd81523bef345cacf34796576f1fdf74b..d30ec21c6ff112fe476074ef280dd273a2373a7f 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -79,7 +79,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -110,6 +110,9 @@
     <li>
       <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
@@ -150,6 +153,8 @@
         <dd></dt>
         <dt><a href="pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a></dt>
         <dd></dt>
+        <dt><a href="pkdown/SeuratWorkflow.html">Seurat workflow</a></dt>
+        <dd></dt>
         <dt><a href="pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a></dt>
         <dd></dt>
       </dl>
diff --git a/docs/articles/pkdown/FAQs.html b/docs/articles/pkdown/FAQs.html
index d8ca90b656dbc3540d5278cd750bf003e1045abf..4c30ddbf77b6210fc365a35210af68e1a5a08d4d 100644
--- a/docs/articles/pkdown/FAQs.html
+++ b/docs/articles/pkdown/FAQs.html
@@ -38,7 +38,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -69,6 +69,9 @@
     <li>
       <a href="../../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/articles/pkdown/SCHNAPPs_usage.html b/docs/articles/pkdown/SCHNAPPs_usage.html
index 47b0441b13f9b8f3c192f6fe055f36337822ce59..751b4d2e9be385b68d77257bdd4481d743ba0845 100644
--- a/docs/articles/pkdown/SCHNAPPs_usage.html
+++ b/docs/articles/pkdown/SCHNAPPs_usage.html
@@ -38,7 +38,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -69,6 +69,9 @@
     <li>
       <a href="../../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
@@ -97,7 +100,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>SCHNAPPs - Single Cell sHiNy APP(s)</h1>
             
-            <h4 class="date">2020-06-07</h4>
+            <h4 class="date">2020-06-09</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/vignettes/pkdown/SCHNAPPs_usage.Rmd"><code>vignettes/pkdown/SCHNAPPs_usage.Rmd</code></a></small>
       <div class="hidden name"><code>SCHNAPPs_usage.Rmd</code></div>
diff --git a/docs/articles/pkdown/scranWorkflow.html b/docs/articles/pkdown/scranWorkflow.html
index 1177ac380b7ba8a6b1a4c92b3900ef2ae41f4736..27e62a1fe8e4883cdff50ee5883a7d5e32f4b59f 100644
--- a/docs/articles/pkdown/scranWorkflow.html
+++ b/docs/articles/pkdown/scranWorkflow.html
@@ -38,7 +38,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -69,6 +69,9 @@
     <li>
       <a href="../../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
@@ -364,7 +367,7 @@ Cluster assignment comparison using 2D plot
 Co-expression - All clusters; After list of gene names has been set to empty SCHNAPPs will automatically fill the list with characteristic genes for each cluster.
 </p>
 </div>
-<p>The following video shows how to use the heatmap module. If the field with the gene names is empty the the function FindMarkers is used to identify the genes that are most characteristic for each cluster. This list of genes is used for the heatmap.</p>
+<p>The following video shows how to use the heatmap module. If the field with the gene names is empty the function FindMarkers is used to identify the genes that are most characteristic for each cluster. This list of genes is used for the heatmap.</p>
 <iframe src="https://www.youtube.com/embed/aiKPccCmZgk" width="420" height="315" frameborder="0" allowfullscreen=""></iframe>
 <p>The genes CPA1, CTRB1, PLA2G1B, PRSS1, PRSS3P2 are highly expressed in cluster 2. GCG, TTR are highly expressed in cluster 5.</p>
 </div>
diff --git a/docs/authors.html b/docs/authors.html
index e443dda2a3ef420cdb4c2ea8a3aae38320541a1f..a45852364a47ebd9e19030b71e1c976d3d8a587b 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -79,7 +79,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -110,6 +110,9 @@
     <li>
       <a href="articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/index.html b/docs/index.html
index 18c86775b10a5b2069992d911d9276cd9845facd..f1547976e6bb2f70e3bce392ec11d0bac1c87f47 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -41,7 +41,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -72,6 +72,9 @@
     <li>
       <a href="articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 20c62ba35370fee9b8a919c7718b08d5670f89a3..c34316a4616517ce8eb88e2f8ab562b8514fc18b 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -5,6 +5,7 @@ articles:
   Readme: Readme.html
   FAQs: pkdown/FAQs.html
   SCHNAPPs_usage: pkdown/SCHNAPPs_usage.html
+  SeuratWorkflow: pkdown/SeuratWorkflow.html
   scranWorkflow: pkdown/scranWorkflow.html
-last_built: 2020-06-07T09:57Z
+last_built: 2020-06-09T09:43Z
 
diff --git a/docs/reference/beforeFilterPrj.html b/docs/reference/beforeFilterPrj.html
deleted file mode 100644
index 15d3b5b0cb314882c30a4d0521e5029962c0675a..0000000000000000000000000000000000000000
--- a/docs/reference/beforeFilterPrj.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>* `beforeFilterPrj` : number of reads that got filtered out — beforeFilterPrj • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="* `beforeFilterPrj` : number of reads that got filtered out — beforeFilterPrj" />
-<meta property="og:description" content="* `beforeFilterPrj` : number of reads that got filtered out" />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>* `beforeFilterPrj` : number of reads that got filtered out</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>beforeFilterPrj.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>* `beforeFilterPrj` : number of reads that got filtered out</p>
-    </div>
-
-    <pre class="usage"><span class='no'>beforeFilterPrj</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>List with "x", "var_pcs", "rotation"</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/reference/ccol.html b/docs/reference/ccol.html
deleted file mode 100644
index dce41dc1288f47865e9a28dec0f96d478691f599..0000000000000000000000000000000000000000
--- a/docs/reference/ccol.html
+++ /dev/null
@@ -1,193 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>Example data for schnapps app — ccol • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="Example data for schnapps app — ccol" />
-<meta property="og:description" content="A dataset containing the prices and other attributes of almost 54,000
-diamonds. The variables are as follows:" />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Example data for schnapps app</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>ccol.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>A dataset containing the prices and other attributes of almost 54,000
-diamonds. The variables are as follows:</p>
-    </div>
-
-    <pre class="usage"><span class='no'>ccol</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>A data frame with 53940 rows and 10 variables</p>
-<p>a vector with colours used for clusters</p>
-    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
-
-    <p>&lt;http://www.diamondse.info/&gt;
-* `ccol` : color definitions</p>
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>* `scExLite`: singlecellExperiment object</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/reference/dbCluster.html b/docs/reference/dbCluster.html
deleted file mode 100644
index 6513bb1d1e17500ad885db2416f66b30e06ded8d..0000000000000000000000000000000000000000
--- a/docs/reference/dbCluster.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>* `dbCluster` : used clustering — dbCluster • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="* `dbCluster` : used clustering — dbCluster" />
-<meta property="og:description" content="* `dbCluster` : used clustering" />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>* `dbCluster` : used clustering</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>dbCluster.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>* `dbCluster` : used clustering</p>
-    </div>
-
-    <pre class="usage"><span class='no'>dbCluster</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>List with "x", "var_pcs", "rotation"</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/reference/dot-schnappsEnv.html b/docs/reference/dot-schnappsEnv.html
index 3fe65dce533c9ec7f4a30a7d47c73569aeec638e..cdc2df0e22636d8f2ab52486263b5eb6c3fb7911 100644
--- a/docs/reference/dot-schnappsEnv.html
+++ b/docs/reference/dot-schnappsEnv.html
@@ -85,7 +85,7 @@ Environment for package" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -116,6 +116,9 @@ Environment for package" />
     <li>
       <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/reference/geneCount.html b/docs/reference/geneCount.html
deleted file mode 100644
index c8b1f5481172cd188b0783fb31c90bf3be7dca1e..0000000000000000000000000000000000000000
--- a/docs/reference/geneCount.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>* `geneCount` : number of genes per cell. — geneCount • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="* `geneCount` : number of genes per cell. — geneCount" />
-<meta property="og:description" content="* `geneCount` : number of genes per cell." />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>* `geneCount` : number of genes per cell.</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>geneCount.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>* `geneCount` : number of genes per cell.</p>
-    </div>
-
-    <pre class="usage"><span class='no'>geneCount</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>List with "x", "var_pcs", "rotation"</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d51a01d98ab9b99e7bd3e5b1945eaf0f1d997b44..826d4450c536e2ec9c7f39d3329acc2974eaca00 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -79,7 +79,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -110,6 +110,9 @@
     <li>
       <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
@@ -161,24 +164,6 @@
       
       <tr>
         
-        <td>
-          <p><code><a href="beforeFilterPrj.html">beforeFilterPrj</a></code> </p>
-        </td>
-        <td><p>* `beforeFilterPrj` : number of reads that got filtered out</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ccol.html">ccol</a></code> </p>
-        </td>
-        <td><p>Example data for schnapps app</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbCluster.html">dbCluster</a></code> </p>
-        </td>
-        <td><p>* `dbCluster` : used clustering</p></td>
-      </tr><tr>
-        
         <td>
           <p><code><a href="dot-schnappsEnv.html">.schnappsEnv</a></code> <code><a href="dot-schnappsEnv.html">.schnappsEnv</a></code> </p>
         </td>
@@ -186,18 +171,6 @@
 Environment for package</p></td>
       </tr><tr>
         
-        <td>
-          <p><code><a href="geneCount.html">geneCount</a></code> </p>
-        </td>
-        <td><p>* `geneCount` : number of genes per cell.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pca.html">pca</a></code> </p>
-        </td>
-        <td><p>* `pca` : pca results, Eigenvalues and vectors.</p></td>
-      </tr><tr>
-        
         <td>
           <p><code><a href="scEx.html">scEx</a></code> </p>
         </td>
@@ -214,30 +187,6 @@ Environment for package</p></td>
           <p><code><a href="schnappsLite.html">schnappsLite()</a></code> </p>
         </td>
         <td><p>shiny server relevant functions</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="scol.html">scol</a></code> </p>
-        </td>
-        <td><p>* `scol` : color definitions for samples</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="tsne.html">tsne</a></code> </p>
-        </td>
-        <td><p>* `tsne` : tsne projection.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="umapReact.html">umapReact</a></code> </p>
-        </td>
-        <td><p>* `umapReact` : umap projections</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="umiCount.html">umiCount</a></code> </p>
-        </td>
-        <td><p>* `pca` : pca results, Eigenvalues and vectors.</p></td>
       </tr>
     </tbody>
     </table>
diff --git a/docs/reference/pca.html b/docs/reference/pca.html
deleted file mode 100644
index a4db2d8ae935cc432a1b18e7edd8fa89694d3ed9..0000000000000000000000000000000000000000
--- a/docs/reference/pca.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>* `pca` : pca results, Eigenvalues and vectors. — pca • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="* `pca` : pca results, Eigenvalues and vectors. — pca" />
-<meta property="og:description" content="* `pca` : pca results, Eigenvalues and vectors." />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>* `pca` : pca results, Eigenvalues and vectors.</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>pca.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>* `pca` : pca results, Eigenvalues and vectors.</p>
-    </div>
-
-    <pre class="usage"><span class='no'>pca</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>List with "x", "var_pcs", "rotation"</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/reference/scEx.html b/docs/reference/scEx.html
index 821340a10da64ab038ce58acf6a502d7b025762b..0310107b60f50c54fdc54f543eedf8673d8b7d32 100644
--- a/docs/reference/scEx.html
+++ b/docs/reference/scEx.html
@@ -81,7 +81,7 @@ diamonds. The variables are as follows:" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -112,6 +112,9 @@ diamonds. The variables are as follows:" />
     <li>
       <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/reference/schnapps.html b/docs/reference/schnapps.html
index 0132291c61b5496349ba70fadc7a82b7ea8b0aa2..8bb981d7b60292a52809d443ed5716318678800c 100644
--- a/docs/reference/schnapps.html
+++ b/docs/reference/schnapps.html
@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -111,6 +111,9 @@
     <li>
       <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/reference/schnappsLite.html b/docs/reference/schnappsLite.html
index 84744b40a97455cde041ebfbbc9f167dcde259b6..c79b34ffc087fc1838c83fe50124595d52abc3ed 100644
--- a/docs/reference/schnappsLite.html
+++ b/docs/reference/schnappsLite.html
@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.60</span>
       </span>
     </div>
 
@@ -111,6 +111,9 @@
     <li>
       <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
     </li>
+    <li>
+      <a href="../articles/pkdown/SeuratWorkflow.html">Seurat workflow</a>
+    </li>
     <li>
       <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
     </li>
diff --git a/docs/reference/scol.html b/docs/reference/scol.html
deleted file mode 100644
index b8d878441893812c4712de2ab7426775a444f202..0000000000000000000000000000000000000000
--- a/docs/reference/scol.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>* `scol` : color definitions for samples — scol • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="* `scol` : color definitions for samples — scol" />
-<meta property="og:description" content="* `scol` : color definitions for samples" />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>* `scol` : color definitions for samples</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>scol.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>* `scol` : color definitions for samples</p>
-    </div>
-
-    <pre class="usage"><span class='no'>scol</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>a vector of colour values for samples</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/reference/tsne.html b/docs/reference/tsne.html
deleted file mode 100644
index 3789185c915176643695fad186582915380c20e0..0000000000000000000000000000000000000000
--- a/docs/reference/tsne.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>* `tsne` : tsne projection. — tsne • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="* `tsne` : tsne projection. — tsne" />
-<meta property="og:description" content="* `tsne` : tsne projection." />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>* `tsne` : tsne projection.</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>tsne.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>* `tsne` : tsne projection.</p>
-    </div>
-
-    <pre class="usage"><span class='no'>tsne</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>List with "x", "var_pcs", "rotation"</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/reference/umapReact.html b/docs/reference/umapReact.html
deleted file mode 100644
index 610b8019bf9b93f593e700dcd3636b12ebf6b739..0000000000000000000000000000000000000000
--- a/docs/reference/umapReact.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>* `umapReact` : umap projections — umapReact • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="* `umapReact` : umap projections — umapReact" />
-<meta property="og:description" content="* `umapReact` : umap projections" />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>* `umapReact` : umap projections</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>umapReact.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>* `umapReact` : umap projections</p>
-    </div>
-
-    <pre class="usage"><span class='no'>umapReact</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>List with "x", "var_pcs", "rotation"</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/docs/reference/umiCount.html b/docs/reference/umiCount.html
deleted file mode 100644
index bb4f6b8ef4b2df8400b5ab366e6fd5b2a657ffba..0000000000000000000000000000000000000000
--- a/docs/reference/umiCount.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-  <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>* `pca` : pca results, Eigenvalues and vectors. — umiCount • SCHNAPPs</title>
-
-<!-- favicons -->
-<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
-
-<!-- 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="* `pca` : pca results, Eigenvalues and vectors. — umiCount" />
-<meta property="og:description" content="* `pca` : pca results, Eigenvalues and vectors." />
-<meta property="og:image" content="/logo.png" />
-
-
-
-
-<!-- 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-reference-topic">
-      <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">SCHNAPPs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/Readme.html">Readme</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/FAQs.html">Frequently asked questions for common tasks</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/SCHNAPPs_usage.html">SCHNAPPs - Single Cell sHiNy APP(s)</a>
-    </li>
-    <li>
-      <a href="../articles/pkdown/scranWorkflow.html">Follow scran workflow to analyze single-cell RNA-seq data</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-
-      </header>
-
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>* `pca` : pca results, Eigenvalues and vectors.</h1>
-    <small class="dont-index">Source: <a href='https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs/blob/master/R/schnapps-Lite.R'><code>R/schnapps-Lite.R</code></a></small>
-    <div class="hidden name"><code>umiCount.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>* `pca` : pca results, Eigenvalues and vectors.</p>
-    </div>
-
-    <pre class="usage"><span class='no'>umiCount</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>List with "x", "var_pcs", "rotation"</p>
-
-  </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>Developed by Bernd Jagla.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
-      </footer>
-   </div>
-
-  
-
-
-  </body>
-</html>
-
-
diff --git a/inst/app/runDevApp.R b/inst/app/runDevApp.R
index ad94b4f4e079221b57b29bcff66d1fbc0784772c..d4dcf15fcb8581a0fb9a46e6f14677cc5eeab1c7 100644
--- a/inst/app/runDevApp.R
+++ b/inst/app/runDevApp.R
@@ -33,21 +33,27 @@ assign("historyPath", historyPath, envir = .schnappsEnv)
 ls(.schnappsEnv)
 
 
+# Scran parameters
+# defaultValues = list()
+# defaultValues[["coEtgMinExpr"]] = 100
+# defaultValues[["pcaScale"]] = FALSE
+# defaultValues[["cellsFiltersOut"]] = "D2ex_54, D2ex_64, D2ex_93, D2ex_95, D2ex_96, D3en1_8, D3en1_9, D3en1_12, D3en1_14, D3en1_15, D3en1_18, D3en1_19, D3en1_20, D3en1_21, D3en1_22, D3en1_23, D3en1_25, D3en1_31, D3en1_32, D3en1_34, D3en1_35, D3en1_36, D3en1_39, D3en1_43, D3en1_44, D3en1_47, D3en1_51, D3en1_52, D3en1_53, D3en1_57, D3en1_58, D3en1_59, D3en1_61, D3en1_62, D3en1_64, D3en1_66, D3en1_70, D3en1_72, D3en1_74, D3en1_76, D3en1_77, D3en1_78, D3en1_80, D3en1_82, D3en1_86, D3en1_91, D3en1_92, D3en1_95, D3en1_96, D3en2_1, D3en2_4, D3en2_8, D3en2_9, D3en2_10, D3en2_11, D3en2_14, D3en2_15, D3en2_18, D3en2_19, D3en2_20, D3en2_28, D3en2_29, D3en2_34, D3en2_35, D3en2_36, D3en2_40, D3en2_41, D3en2_43, D3en2_44, D3en2_46, D3en2_47, D3en2_49, D3en2_53, D3en2_54, D3en2_59, D3en2_65, D3en2_67, D3en2_69, D3en2_70, D3en2_75, D3en2_76, D3en2_77, D3en2_78, D3en2_79, D3en2_80, D3en2_82, D3en2_84, D3en2_86, D3en2_87, D3en2_88, D3en2_89, D3en2_95, D3en2_96, D3en3_3, D3en3_4, D3en3_12, D3en3_13, D3en3_14, D3en3_15, D3en3_17, D3en3_19, D3en3_20, D3en3_22, D3en3_23, D3en3_24, D3en3_25, D3en3_26, D3en3_31, D3en3_33, D3en3_35, D3en3_37, D3en3_38, D3en3_42, D3en3_43, D3en3_45, D3en3_47, D3en3_49, D3en3_56, D3en3_57, D3en3_58, D3en3_60, D3en3_61, D3en3_62, D3en3_63, D3en3_66, D3en3_69, D3en3_70, D3en3_71, D3en3_76, D3en3_79, D3en3_88, D3en3_90, D3en3_91, D3en3_93, D3en3_96, D3en4_1, D3en4_5, D3en4_10, D3en4_11, D3en4_13, D3en4_15, D3en4_17, D3en4_18, D3en4_21, D3en4_24, D3en4_27, D3en4_28, D3en4_29, D3en4_34, D3en4_36, D3en4_37, D3en4_40, D3en4_44, D3en4_45, D3en4_49, D3en4_50, D3en4_51, D3en4_52, D3en4_53, D3en4_55, D3en4_57, D3en4_59, D3en4_62, D3en4_66, D3en4_67, D3en4_70, D3en4_75, D3en4_76, D3en4_77, D3en4_78, D3en4_79, D3en4_80, D3en4_88, D3en4_93, D3en4_94, D3en4_95, D3ex_1, D3ex_2, D3ex_7, D3ex_8, D3ex_10, D3ex_11, D3ex_13, D3ex_14, D3ex_15, D3ex_17, D3ex_18, D3ex_19, D3ex_20, D3ex_21, D3ex_22, D3ex_23, D3ex_25, D3ex_26, D3ex_27, D3ex_28, D3ex_29, D3ex_30, D3ex_31, D3ex_32, D3ex_33, D3ex_35, D3ex_37, D3ex_38, D3ex_42, D3ex_43, D3ex_44, D3ex_45, D3ex_46, D3ex_47, D3ex_49, D3ex_50, D3ex_52, D3ex_53, D3ex_56, D3ex_57, D3ex_58, D3ex_59, D3ex_60, D3ex_61, D3ex_62, D3ex_63, D3ex_64, D3ex_65, D3ex_67, D3ex_69, D3ex_70, D3ex_72, D3ex_73, D3ex_75, D3ex_78, D3ex_79, D3ex_80, D3ex_81, D3ex_82, D3ex_84, D3ex_85, D3ex_86, D3ex_89, D3ex_93, D3ex_94, D3ex_95, D3ex_96, D74_4, D74_11, D74_19, D74_30, D74_38, D74_50, D74_72, D74_80, D71_13, D71_24, D71_25, D71_46, D71_50, D71_74, D71_77, D71_96, D72_6, D72_17, D72_26, D72_51, D72_56, D72_60, D73_53, D73_66, D73_74, D73_75, D73_77, D73_80, D73_88, D10631_1, D10631_6, D10631_13, D10631_16, D10631_28, D10631_30, D10631_31, D10631_32, D10631_35, D10631_49, D10631_59, D10631_77, D10631_86, D101_2, D101_3, D101_4, D101_6, D101_9, D101_12, D101_15, D101_18, D101_19, D101_20, D101_23, D101_26, D101_30, D101_32, D101_33, D101_38, D101_39, D101_40, D101_41, D101_47, D101_49, D101_54, D101_55, D101_60, D101_61, D101_62, D101_63, D101_64, D101_65, D101_67, D101_68, D101_70, D101_71, D101_75, D101_76, D101_78, D101_79, D101_80, D101_85, D101_86, D101_87, D101_90, D101_92, D101_94, D101_96, D102_2, D102_5, D102_8, D102_9, D102_10, D102_12, D102_13, D102_15, D102_16, D102_19, D102_20, D102_22, D102_23, D102_27, D102_28, D102_29, D102_30, D102_31, D102_32, D102_33, D102_34, D102_35, D102_36, D102_37, D102_38, D102_41, D102_42, D102_43, D102_44, D102_46, D102_48, D102_49, D102_52, D102_53, D102_56, D102_60, D102_62, D102_65, D102_67, D102_70, D102_72, D102_74, D102_77, D102_84, D102_85, D102_88, D102_89, D102_90, D102_92, D102_95, D17All1_13, D17All1_94, D17All2_5, D17All2_50, D17All2_89, D17TGFB_60, D17TGFB_62, D2ex_94, D3en1_40, D3en2_51, D3en3_18, D3en3_40, D3en3_77, D3en3_81, D3en3_83, D3en4_90, D3en4_96, D74_48, D74_84, D74_96, D71_89, D72_94, D73_47, D10631_47, D10631_75, D10631_78, D10631_79, D10631_80, D10631_83, D10631_84, D10631_94, D101_8, D101_11, D101_46, D102_47, D102_80, D102_81, D102_83, D172444_94, D172444_95, D172444_96, D17All1_14, D17All1_15, D17All1_17, D17All1_85, D17All2_96, D17TGFB_96"
+# defaultValues[["selectIds"]] = ""
+# defaultValues[["sampleInput"]] =FALSE
+# defaultValues[["whichscLog"]] = "calcLog"
+# defaultValues[["normalizationRadioButton"]] = "DE_scaterNormalization"
+# defaultValues[["pcaN"]] = 951
+# defaultValues[["tabsetCluster"]] = "snnGraph"
+# defaultValues[["minGenesGS"]] = 1
+# defaultValues[["pcaRank"]] = 14
+# defaultValues[["minGenes"]] = 1
+# defaultValues[["alluiv1"]] = "cluster"
+# defaultValues[["alluiv2"]] = "dbCluster"
+
+# Seurat parameters
 defaultValues = list()
-defaultValues[["coEtgMinExpr"]] = 100
-defaultValues[["pcaScale"]] = FALSE
-defaultValues[["cellsFiltersOut"]] = "D2ex_54, D2ex_64, D2ex_93, D2ex_95, D2ex_96, D3en1_8, D3en1_9, D3en1_12, D3en1_14, D3en1_15, D3en1_18, D3en1_19, D3en1_20, D3en1_21, D3en1_22, D3en1_23, D3en1_25, D3en1_31, D3en1_32, D3en1_34, D3en1_35, D3en1_36, D3en1_39, D3en1_43, D3en1_44, D3en1_47, D3en1_51, D3en1_52, D3en1_53, D3en1_57, D3en1_58, D3en1_59, D3en1_61, D3en1_62, D3en1_64, D3en1_66, D3en1_70, D3en1_72, D3en1_74, D3en1_76, D3en1_77, D3en1_78, D3en1_80, D3en1_82, D3en1_86, D3en1_91, D3en1_92, D3en1_95, D3en1_96, D3en2_1, D3en2_4, D3en2_8, D3en2_9, D3en2_10, D3en2_11, D3en2_14, D3en2_15, D3en2_18, D3en2_19, D3en2_20, D3en2_28, D3en2_29, D3en2_34, D3en2_35, D3en2_36, D3en2_40, D3en2_41, D3en2_43, D3en2_44, D3en2_46, D3en2_47, D3en2_49, D3en2_53, D3en2_54, D3en2_59, D3en2_65, D3en2_67, D3en2_69, D3en2_70, D3en2_75, D3en2_76, D3en2_77, D3en2_78, D3en2_79, D3en2_80, D3en2_82, D3en2_84, D3en2_86, D3en2_87, D3en2_88, D3en2_89, D3en2_95, D3en2_96, D3en3_3, D3en3_4, D3en3_12, D3en3_13, D3en3_14, D3en3_15, D3en3_17, D3en3_19, D3en3_20, D3en3_22, D3en3_23, D3en3_24, D3en3_25, D3en3_26, D3en3_31, D3en3_33, D3en3_35, D3en3_37, D3en3_38, D3en3_42, D3en3_43, D3en3_45, D3en3_47, D3en3_49, D3en3_56, D3en3_57, D3en3_58, D3en3_60, D3en3_61, D3en3_62, D3en3_63, D3en3_66, D3en3_69, D3en3_70, D3en3_71, D3en3_76, D3en3_79, D3en3_88, D3en3_90, D3en3_91, D3en3_93, D3en3_96, D3en4_1, D3en4_5, D3en4_10, D3en4_11, D3en4_13, D3en4_15, D3en4_17, D3en4_18, D3en4_21, D3en4_24, D3en4_27, D3en4_28, D3en4_29, D3en4_34, D3en4_36, D3en4_37, D3en4_40, D3en4_44, D3en4_45, D3en4_49, D3en4_50, D3en4_51, D3en4_52, D3en4_53, D3en4_55, D3en4_57, D3en4_59, D3en4_62, D3en4_66, D3en4_67, D3en4_70, D3en4_75, D3en4_76, D3en4_77, D3en4_78, D3en4_79, D3en4_80, D3en4_88, D3en4_93, D3en4_94, D3en4_95, D3ex_1, D3ex_2, D3ex_7, D3ex_8, D3ex_10, D3ex_11, D3ex_13, D3ex_14, D3ex_15, D3ex_17, D3ex_18, D3ex_19, D3ex_20, D3ex_21, D3ex_22, D3ex_23, D3ex_25, D3ex_26, D3ex_27, D3ex_28, D3ex_29, D3ex_30, D3ex_31, D3ex_32, D3ex_33, D3ex_35, D3ex_37, D3ex_38, D3ex_42, D3ex_43, D3ex_44, D3ex_45, D3ex_46, D3ex_47, D3ex_49, D3ex_50, D3ex_52, D3ex_53, D3ex_56, D3ex_57, D3ex_58, D3ex_59, D3ex_60, D3ex_61, D3ex_62, D3ex_63, D3ex_64, D3ex_65, D3ex_67, D3ex_69, D3ex_70, D3ex_72, D3ex_73, D3ex_75, D3ex_78, D3ex_79, D3ex_80, D3ex_81, D3ex_82, D3ex_84, D3ex_85, D3ex_86, D3ex_89, D3ex_93, D3ex_94, D3ex_95, D3ex_96, D74_4, D74_11, D74_19, D74_30, D74_38, D74_50, D74_72, D74_80, D71_13, D71_24, D71_25, D71_46, D71_50, D71_74, D71_77, D71_96, D72_6, D72_17, D72_26, D72_51, D72_56, D72_60, D73_53, D73_66, D73_74, D73_75, D73_77, D73_80, D73_88, D10631_1, D10631_6, D10631_13, D10631_16, D10631_28, D10631_30, D10631_31, D10631_32, D10631_35, D10631_49, D10631_59, D10631_77, D10631_86, D101_2, D101_3, D101_4, D101_6, D101_9, D101_12, D101_15, D101_18, D101_19, D101_20, D101_23, D101_26, D101_30, D101_32, D101_33, D101_38, D101_39, D101_40, D101_41, D101_47, D101_49, D101_54, D101_55, D101_60, D101_61, D101_62, D101_63, D101_64, D101_65, D101_67, D101_68, D101_70, D101_71, D101_75, D101_76, D101_78, D101_79, D101_80, D101_85, D101_86, D101_87, D101_90, D101_92, D101_94, D101_96, D102_2, D102_5, D102_8, D102_9, D102_10, D102_12, D102_13, D102_15, D102_16, D102_19, D102_20, D102_22, D102_23, D102_27, D102_28, D102_29, D102_30, D102_31, D102_32, D102_33, D102_34, D102_35, D102_36, D102_37, D102_38, D102_41, D102_42, D102_43, D102_44, D102_46, D102_48, D102_49, D102_52, D102_53, D102_56, D102_60, D102_62, D102_65, D102_67, D102_70, D102_72, D102_74, D102_77, D102_84, D102_85, D102_88, D102_89, D102_90, D102_92, D102_95, D17All1_13, D17All1_94, D17All2_5, D17All2_50, D17All2_89, D17TGFB_60, D17TGFB_62, D2ex_94, D3en1_40, D3en2_51, D3en3_18, D3en3_40, D3en3_77, D3en3_81, D3en3_83, D3en4_90, D3en4_96, D74_48, D74_84, D74_96, D71_89, D72_94, D73_47, D10631_47, D10631_75, D10631_78, D10631_79, D10631_80, D10631_83, D10631_84, D10631_94, D101_8, D101_11, D101_46, D102_47, D102_80, D102_81, D102_83, D172444_94, D172444_95, D172444_96, D17All1_14, D17All1_15, D17All1_17, D17All1_85, D17All2_96, D17TGFB_96"
-defaultValues[["selectIds"]] = ""
-defaultValues[["sampleInput"]] =FALSE
-defaultValues[["whichscLog"]] = "calcLog"
-defaultValues[["normalizationRadioButton"]] = "DE_scaterNormalization"
-defaultValues[["pcaN"]] = 951
-defaultValues[["tabsetCluster"]] = "snnGraph"
-defaultValues[["minGenesGS"]] = 1
-defaultValues[["pcaRank"]] = 14
-defaultValues[["minGenes"]] = 1
-defaultValues[["alluiv1"]] = "cluster"
-defaultValues[["alluiv2"]] = "dbCluster"
+defaultValues[["cellsFiltersOut"]] = "AAAGATCTGGGCAA-1, AAAGCAGAAGCCAT-1, AACGCCCTGCTTAG-1, AAGGTCTGGTATGC-1, AATGTAACGTTTGG-1, AATTACGAGTAGCT-1, ACACAGACACCTGA-1, ACATGGTGCGTTGA-1, ACCTGGCTGTCTTT-1, ACTTAAGACCACAA-1, ACTTGTACCCGAAT-1, ACTTTGTGCGATAC-1, AGAGGTCTACAGCT-1, ATCACGGATTGCTT-1, ATTACCTGGGCATT-1, CACGCTACTTGACG-1, CAGTGTGAACACGT-1, CCAATGGAACAGCT-1, CCAGTCTGCGGAGA-1, CGACCTTGGCAAGG-1, CGAGCCGACGACAT-1, CGGAATTGCACTAG-1, CGTAACGAATCAGC-1, CGTACCACGCTACA-1, CGTACCTGGACGAG-1, CTAGTTTGAGTACC-1, CTCAGCTGTTTCTG-1, CTCATTGATTGCTT-1, CTGGCACTGGACAG-1, CTTAACACGAGCTT-1, CTTAAGCTTCCTCG-1, GAAAGATGTTTGCT-1, GAACGTTGACGGAG-1, GAATGGCTAAGATG-1, GACCATGACTCTCG-1, GACTGAACAACCGT-1, GCCACTACCTACTT-1, GCGAAGGAGAGCTT-1, GCTACAGATCTTAC-1, GGCACGTGTGAGAA-1, GTCAACGATCAGGT-1, GTGAACACAGATCC-1, GTGTCAGAATGCTG-1, GTTAAAACTTCGCC-1, TAAGATACCCACAA-1, TACGCAGACGTCTC-1, TACGCGCTCTTCTA-1, TACGGCCTGTCCTC-1, TATCACTGACTGTG-1, TCCCGATGCTGTGA-1, TCGCACACCATCAG-1, TCGTGAGAACTGTG-1, TGAAGCTGAGACTC-1, TGAGACACTGTGCA-1, TGAGCTGAGCGAGA-1, TGGAGACTGAAACA-1, TGGATGTGATGTCG-1, TGGCAATGGAGGGT-1, TGGTCAGACCGTTC-1, TGTTAAGATTGGCA-1, TTACTCGAACGTTG-1, TTCAAGCTTCCAAG-1"
+
 
 
 assign("defaultValues", defaultValues, envir = .schnappsEnv)
diff --git a/inst/develo/georacle.R b/inst/develo/georacle.R
new file mode 100644
index 0000000000000000000000000000000000000000..c07ec56ed3f01781c4cb24b2a34029d2dc03767f
--- /dev/null
+++ b/inst/develo/georacle.R
@@ -0,0 +1,6 @@
+install.packages("devtools")
+library(devtools)
+devtools::install_github("VCCRI/Georacle")
+
+
+Georacle::Georacle()
diff --git a/man/beforeFilterPrj.Rd b/man/beforeFilterPrj.Rd
deleted file mode 100644
index 2d65b6ca3016f3dd0d787abfe871d1b5ed1accff..0000000000000000000000000000000000000000
--- a/man/beforeFilterPrj.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{beforeFilterPrj}
-\alias{beforeFilterPrj}
-\title{* `beforeFilterPrj` : number of reads that got filtered out}
-\format{
-List with "x", "var_pcs", "rotation"
-}
-\usage{
-beforeFilterPrj
-}
-\description{
-* `beforeFilterPrj` : number of reads that got filtered out
-}
-\keyword{datasets}
diff --git a/man/ccol.Rd b/man/ccol.Rd
deleted file mode 100644
index cbb4092b780c309ea75354d87244b38a7664318c..0000000000000000000000000000000000000000
--- a/man/ccol.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{ccol}
-\alias{ccol}
-\title{Example data for schnapps app}
-\format{
-A data frame with 53940 rows and 10 variables
-
-a vector with colours used for clusters
-}
-\source{
-<http://www.diamondse.info/>
-* `ccol` : color definitions
-}
-\usage{
-ccol
-}
-\description{
-A dataset containing the prices and other attributes of almost 54,000
-diamonds. The variables are as follows:
-}
-\details{
-* `scExLite`: singlecellExperiment object
-}
-\keyword{datasets}
diff --git a/man/dbCluster.Rd b/man/dbCluster.Rd
deleted file mode 100644
index 2adf273afd949c6f4feb55e3d95b5e642a17f7d8..0000000000000000000000000000000000000000
--- a/man/dbCluster.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{dbCluster}
-\alias{dbCluster}
-\title{* `dbCluster` : used clustering}
-\format{
-List with "x", "var_pcs", "rotation"
-}
-\usage{
-dbCluster
-}
-\description{
-* `dbCluster` : used clustering
-}
-\keyword{datasets}
diff --git a/man/geneCount.Rd b/man/geneCount.Rd
deleted file mode 100644
index 23df638a07261a726e65c62b1c47210456ab6b41..0000000000000000000000000000000000000000
--- a/man/geneCount.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{geneCount}
-\alias{geneCount}
-\title{* `geneCount` : number of genes per cell.}
-\format{
-List with "x", "var_pcs", "rotation"
-}
-\usage{
-geneCount
-}
-\description{
-* `geneCount` : number of genes per cell.
-}
-\keyword{datasets}
diff --git a/man/pca.Rd b/man/pca.Rd
deleted file mode 100644
index 2e89a509ba3496825c1cb043828328005d8a583c..0000000000000000000000000000000000000000
--- a/man/pca.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{pca}
-\alias{pca}
-\title{* `pca` : pca results, Eigenvalues and vectors.}
-\format{
-List with "x", "var_pcs", "rotation"
-}
-\usage{
-pca
-}
-\description{
-* `pca` : pca results, Eigenvalues and vectors.
-}
-\keyword{datasets}
diff --git a/man/scol.Rd b/man/scol.Rd
deleted file mode 100644
index d95692c48d2f693ee69860f5846ef3cb5e85462d..0000000000000000000000000000000000000000
--- a/man/scol.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{scol}
-\alias{scol}
-\title{* `scol` : color definitions for samples}
-\format{
-a vector of colour values for samples
-}
-\usage{
-scol
-}
-\description{
-* `scol` : color definitions for samples
-}
-\keyword{datasets}
diff --git a/man/tsne.Rd b/man/tsne.Rd
deleted file mode 100644
index fe880991c9958e00cbc5c40ea40996d184858630..0000000000000000000000000000000000000000
--- a/man/tsne.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{tsne}
-\alias{tsne}
-\title{* `tsne` : tsne projection.}
-\format{
-List with "x", "var_pcs", "rotation"
-}
-\usage{
-tsne
-}
-\description{
-* `tsne` : tsne projection.
-}
-\keyword{datasets}
diff --git a/man/umapReact.Rd b/man/umapReact.Rd
deleted file mode 100644
index 36e3fb7163bfc52400ec96f35e4c1fe38cf2496c..0000000000000000000000000000000000000000
--- a/man/umapReact.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{umapReact}
-\alias{umapReact}
-\title{* `umapReact` : umap projections}
-\format{
-List with "x", "var_pcs", "rotation"
-}
-\usage{
-umapReact
-}
-\description{
-* `umapReact` : umap projections
-}
-\keyword{datasets}
diff --git a/man/umiCount.Rd b/man/umiCount.Rd
deleted file mode 100644
index c537add7c60d8229ef14d791c065c715b435d799..0000000000000000000000000000000000000000
--- a/man/umiCount.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schnapps-Lite.R
-\docType{data}
-\name{umiCount}
-\alias{umiCount}
-\title{* `pca` : pca results, Eigenvalues and vectors.}
-\format{
-List with "x", "var_pcs", "rotation"
-}
-\usage{
-umiCount
-}
-\description{
-* `pca` : pca results, Eigenvalues and vectors.
-}
-\keyword{datasets}
diff --git a/vignettes/pkdown/SeuratWorkflow.Rmd b/vignettes/pkdown/SeuratWorkflow.Rmd
new file mode 100644
index 0000000000000000000000000000000000000000..c3ba17517002ca2a3eab0d1952d57ee05e934feb
--- /dev/null
+++ b/vignettes/pkdown/SeuratWorkflow.Rmd
@@ -0,0 +1,95 @@
+---
+title: "Seurat workflow"
+author: 
+- name: Bernd Jagla
+  email: bernd <DOT> jagla <AT> pasteur <DOT> fr
+date: "6/7/2020"
+output: 
+  html_document:
+    code_folding: hide
+package: SCHNAPPs
+bibliography: ref.bib
+vignette: >
+  %\VignetteIndexEntry{Follow Seurat workflow}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}    
+---
+
+
+
+```{r, echo=FALSE, results="hide", message=FALSE}
+require(knitr)
+library("htmltools")
+library("vembedr")
+opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)
+```
+
+Please see the scran workflow for a more indepth workflow.
+
+```{r}
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(SCHNAPPs)
+library(SingleCellExperiment)
+# Load the PBMC dataset
+pbmc.data <- Read10X(data.dir = "~/Downloads/filtered_gene_bc_matrices/hg19/")
+# Initialize the Seurat object with the raw (non-normalized data).
+pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)
+pbmc
+
+pbmc[["percent.mt"]] <- PercentageFeatureSet(pbmc, pattern = "^MT-")
+
+scEx = as.SingleCellExperiment(pbmc)
+
+colnames(colData(scEx)) = c("sampleNames",   "nCount_RNA",   "nFeature_RNA", "percent.mt" , "ident"       )
+colData(scEx)$barcode = rownames(colData(scEx))
+
+rowData(scEx)$Description = ""
+rowData(scEx)$id = rownames(rowData(scEx))
+rowData(scEx)$symbol = rownames(rowData(scEx))
+
+
+```
+
+```{r seuratCont}
+
+pbmc <- subset(pbmc, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5)
+pbmc <- NormalizeData(pbmc)
+pbmc <- FindVariableFeatures(pbmc, selection.method = "vst", nfeatures = 2000)
+
+top10 <- head(VariableFeatures(pbmc), 10)
+
+all.genes <- rownames(pbmc)
+pbmc <- ScaleData(pbmc, features = all.genes)
+
+pbmc <- RunPCA(pbmc, features = VariableFeatures(object = pbmc))
+
+
+pbmc <- FindNeighbors(pbmc, dims = 1:10)
+pbmc <- FindClusters(pbmc, resolution = 0.5)
+
+pbmc <- RunUMAP(pbmc, dims = 1:10)
+
+colData(scEx)$seurartCluster = -1
+colData(scEx)[names(Idents(pbmc)),"seurartCluster"] = Idents(pbmc)
+colData(scEx)$seurartCluster = as.factor(colData(scEx)$seurartCluster)
+
+```
+
+
+
+```{r save file,  cache=TRUE, eval=FALSE}
+save(file = "seurat.pbmc.RData", list = c("scEx"))
+```
+
+
+
+
+Zooming into the low nFeatureRNA region reveals that no cells will be removed using the 200 threshold.
+
+```{r, out.width='90%', fig.align='center', fig.cap='Filter based on detected genes', echo=FALSE}
+knitr::include_graphics('images/2Dzoomed.png')
+```
+
+
diff --git a/vignettes/pkdown/images/2Dzoomed.png b/vignettes/pkdown/images/2Dzoomed.png
new file mode 100644
index 0000000000000000000000000000000000000000..2726489aa1b6d09ee058a63e13fe3cb77da3cb39
Binary files /dev/null and b/vignettes/pkdown/images/2Dzoomed.png differ