enrichmentPanel

enrichmentPanelUI

enrichmentPanelServer

These are the UI and server components of the enrichment panel of the
shiny app. It is generated by including 'Enrichment' in the panels.default argument
of <code>generateShinyApp</code>.

Given an expression matrix from a bulk sequencing experiment,
pre-processes it and creates a shiny app for interactive data
analysis and visualisation. The app contains quality checks,
differential expression analysis, volcano and cross plots,
enrichment analysis and gene regulatory network inference,
and can be customised to contain more panels by the user.

Ilias Moutsopoulos

bulkAnalyseR

Interactive Shiny App for Bulk Sequencing Data

Eleanor Williams

Irina Mohorianu

enrichmentPanel function

<dl><dt>id</dt>
<dd>the input slot that will be used to access the value</dd>
<dt>show</dt>
<dd>whether to show the panel or not; default is TRUE; there for
compatibility with specifying panels to show</dd>
<dt>DEresults</dt>
<dd>differential expression results output from DEpanelServer;
a reactive list with slots 'DEtable' (all genes), 'DEtableSubset' (only DE genes),
'lfcThreshold' and 'pvalThreshold'</dd>
<dt>organism</dt>
<dd>organism name to be passed on to <code>gprofiler2::gost</code>;
organism names are constructed by concatenating the first letter of the
name and the family name; default is NA - enrichment is not included
to ensure compatibility with datasets that have non-standard gene names;
a vector (of the same length as modality) can be provided if
<code>length(modality) &gt; 1</code></dd>
<dt>seed</dt>
<dd>the random seed to be set for the jitter plot, to avoid
seemingly different plots for the same inputs</dd></dl>

Arguments

Generate the enrichment panel of the shiny app — enrichmentPanel

<dl>

<dt>id</dt>
<dd>the input slot that will be used to access the value</dd>


<dt>show</dt>
<dd>whether to show the panel or not; default is TRUE; there for
compatibility with specifying panels to show</dd>


<dt>DEresults</dt>
<dd>differential expression results output from DEpanelServer;
a reactive list with slots 'DEtable' (all genes), 'DEtableSubset' (only DE genes),
'lfcThreshold' and 'pvalThreshold'</dd>


<dt>organism</dt>
<dd>organism name to be passed on to <code>gprofiler2::gost</code>;
organism names are constructed by concatenating the first letter of the
name and the family name; default is NA - enrichment is not included
to ensure compatibility with datasets that have non-standard gene names;
a vector (of the same length as modality) can be provided if
<code>length(modality) &gt; 1</code></dd>


<dt>seed</dt>
<dd>the random seed to be set for the jitter plot, to avoid
seemingly different plots for the same inputs</dd>

</dl>

enrichmentPanel: Generate the enrichment panel of the shiny app

Description

Usage

Value

Arguments