webP2proc

Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.

Evan Biederstedt

pagoda2

Single Cell Analysis and Differential Expression

Nikolas Barkas

Viktor Petukhov

Peter Kharchenko

Simon Steiger

Rasmus Rydbirk

webP2proc function

<dl><dt>p2</dt>
<dd>a 'Pagoda2' object</dd>
<dt>additionalMetadata</dt>
<dd>'pagoda2' web metadata object (default=NULL)</dd>
<dt>title</dt>
<dd>character string Title for the web app (default='Pagoda2')</dd>
<dt>make.go.sets</dt>
<dd>boolean Whether GO sets should be made (default=TRUE)</dd>
<dt>make.de.sets</dt>
<dd>boolean Whether differential expression sets should be made (default=TRUE)</dd>
<dt>go.env</dt>
<dd>the GO environment used for the overdispersion analysis (default=NULL)</dd>
<dt>make.gene.graph</dt>
<dd>logical specifying if the gene graph should be make, if FALSE the find similar genes functionality will be disabled on the web app</dd>
<dt>appmetadata</dt>
<dd>'pagoda2' web application metadata (default=NULL)</dd></dl>

Arguments

Generate a 'pagoda2' web object — webP2proc

<dl>

<dt>p2</dt>
<dd>a 'Pagoda2' object</dd>


<dt>additionalMetadata</dt>
<dd>'pagoda2' web metadata object (default=NULL)</dd>


<dt>title</dt>
<dd>character string Title for the web app (default='Pagoda2')</dd>


<dt>make.go.sets</dt>
<dd>boolean Whether GO sets should be made (default=TRUE)</dd>


<dt>make.de.sets</dt>
<dd>boolean Whether differential expression sets should be made (default=TRUE)</dd>


<dt>go.env</dt>
<dd>the GO environment used for the overdispersion analysis (default=NULL)</dd>


<dt>make.gene.graph</dt>
<dd>logical specifying if the gene graph should be make, if FALSE the find similar genes functionality will be disabled on the web app</dd>


<dt>appmetadata</dt>
<dd>'pagoda2' web application metadata (default=NULL)</dd>

</dl>

Generate a 'pagoda2' web object

webP2proc: Generate a 'pagoda2' web object

Description

Usage

Value

Arguments