From 1f419641da86b3dc1dda71a7cadf16f289236b2f Mon Sep 17 00:00:00 2001
From: Bernd Jagla <bernd.jagla@pasteur.fr>
Date: Tue, 9 Jun 2020 11:38:48 +0200
Subject: [PATCH] new docs
---
.gitignore | 2 +
DESCRIPTION | 2 +-
R/schnapps-Lite.R | 62 --------
docs/404.html | 5 +-
docs/CONTRIBUTING.html | 5 +-
docs/articles/Readme.html | 5 +-
docs/articles/index.html | 7 +-
docs/articles/pkdown/FAQs.html | 5 +-
docs/articles/pkdown/SCHNAPPs_usage.html | 7 +-
docs/articles/pkdown/scranWorkflow.html | 7 +-
docs/authors.html | 5 +-
docs/index.html | 5 +-
docs/pkgdown.yml | 3 +-
docs/reference/beforeFilterPrj.html | 183 ---------------------
docs/reference/ccol.html | 193 -----------------------
docs/reference/dbCluster.html | 183 ---------------------
docs/reference/dot-schnappsEnv.html | 5 +-
docs/reference/geneCount.html | 183 ---------------------
docs/reference/index.html | 59 +------
docs/reference/pca.html | 183 ---------------------
docs/reference/scEx.html | 5 +-
docs/reference/schnapps.html | 5 +-
docs/reference/schnappsLite.html | 5 +-
docs/reference/scol.html | 183 ---------------------
docs/reference/tsne.html | 183 ---------------------
docs/reference/umapReact.html | 183 ---------------------
docs/reference/umiCount.html | 183 ---------------------
inst/app/runDevApp.R | 34 ++--
inst/develo/georacle.R | 6 +
man/beforeFilterPrj.Rd | 16 --
man/ccol.Rd | 26 ---
man/dbCluster.Rd | 16 --
man/geneCount.Rd | 16 --
man/pca.Rd | 16 --
man/scol.Rd | 16 --
man/tsne.Rd | 16 --
man/umapReact.Rd | 16 --
man/umiCount.Rd | 16 --
vignettes/pkdown/SeuratWorkflow.Rmd | 95 +++++++++++
vignettes/pkdown/images/2Dzoomed.png | Bin 0 -> 44867 bytes
40 files changed, 186 insertions(+), 1959 deletions(-)
delete mode 100644 docs/reference/beforeFilterPrj.html
delete mode 100644 docs/reference/ccol.html
delete mode 100644 docs/reference/dbCluster.html
delete mode 100644 docs/reference/geneCount.html
delete mode 100644 docs/reference/pca.html
delete mode 100644 docs/reference/scol.html
delete mode 100644 docs/reference/tsne.html
delete mode 100644 docs/reference/umapReact.html
delete mode 100644 docs/reference/umiCount.html
create mode 100644 inst/develo/georacle.R
delete mode 100644 man/beforeFilterPrj.Rd
delete mode 100644 man/ccol.Rd
delete mode 100644 man/dbCluster.Rd
delete mode 100644 man/geneCount.Rd
delete mode 100644 man/pca.Rd
delete mode 100644 man/scol.Rd
delete mode 100644 man/tsne.Rd
delete mode 100644 man/umapReact.Rd
delete mode 100644 man/umiCount.Rd
create mode 100644 vignettes/pkdown/SeuratWorkflow.Rmd
create mode 100644 vignettes/pkdown/images/2Dzoomed.png
diff --git a/.gitignore b/.gitignore
index 00b624d..8f2e298 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 d9b9ea7..6ce7e60 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 7ee4ca5..8e4eb84 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 340665c..a11755c 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 afacc79..3f3d1fb 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 abc822a..4adea7d 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 2829dbe..d30ec21 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 d8ca90b..4c30ddb 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 47b0441..751b4d2 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 1177ac3..27e62a1 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 e443dda..a458523 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 18c8677..f154797 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 20c62ba..c34316a 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 15d3b5b..0000000
--- 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/">
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-
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-
-
-
- </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">
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diff --git a/docs/reference/ccol.html b/docs/reference/ccol.html
deleted file mode 100644
index dce41dc..0000000
--- a/docs/reference/ccol.html
+++ /dev/null
@@ -1,193 +0,0 @@
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-<!DOCTYPE html>
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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
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- <div id="navbar" class="navbar-collapse collapse">
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- <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/">
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-</li>
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-
- </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><http://www.diamondse.info/>
-* `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>
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diff --git a/docs/reference/dbCluster.html b/docs/reference/dbCluster.html
deleted file mode 100644
index 6513bb1..0000000
--- 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">
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-<title>* `dbCluster` : used clustering — dbCluster • SCHNAPPs</title>
-
-<!-- favicons -->
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-
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-
-<!-- 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>
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-<!-- headroom.js -->
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- <a href="../articles/Readme.html">Readme</a>
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- <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>
-
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- </div><!--/.container -->
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-
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- </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">
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- <h2 data-toc-skip>Contents</h2>
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diff --git a/docs/reference/dot-schnappsEnv.html b/docs/reference/dot-schnappsEnv.html
index 3fe65dc..cdc2df0 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 c8b1f54..0000000
--- a/docs/reference/geneCount.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<title>* `geneCount` : number of genes per cell. — geneCount • SCHNAPPs</title>
-
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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.59</span>
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- Articles
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- <a href="../articles/Readme.html">Readme</a>
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- <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/">
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- </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>
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- <footer>
- <div class="copyright">
- <p>Developed by Bernd Jagla.</p>
-</div>
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index d51a01d..826d445 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 a4db2d8..0000000
--- a/docs/reference/pca.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
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-<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">
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-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
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- <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>
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- <a href="../index.html">
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- <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>
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- </a>
-</li>
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-
- </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>
-
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- </div>
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-</html>
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diff --git a/docs/reference/scEx.html b/docs/reference/scEx.html
index 821340a..0310107 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 0132291..8bb981d 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 84744b4..c79b34f 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 b8d8784..0000000
--- 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">
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-<!-- jquery -->
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- <pre class="usage"><span class='no'>umapReact</span></pre>
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- <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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- <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>
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- <p>* `pca` : pca results, Eigenvalues and vectors.</p>
- </div>
-
- <pre class="usage"><span class='no'>umiCount</span></pre>
-
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- <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
- <p>List with "x", "var_pcs", "rotation"</p>
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diff --git a/inst/app/runDevApp.R b/inst/app/runDevApp.R
index ad94b4f..d4dcf15 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 0000000..c07ec56
--- /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 2d65b6c..0000000
--- 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 cbb4092..0000000
--- 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 2adf273..0000000
--- 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 23df638..0000000
--- 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 2e89a50..0000000
--- 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 d95692c..0000000
--- 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 fe88099..0000000
--- 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 36e3fb7..0000000
--- 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 c537add..0000000
--- 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 0000000..c3ba175
--- /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
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--
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