dprocess_dgeList

This function filters out low-expressed genes from a <code>DGEList</code> object and
normalizes the count data. It also provides diagnostic plots for raw and
filtered data.

Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi: 10.1093/nar/gkac947>). Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi: 10.1101/2024.09.14.609619> for more details.

Wei Cui

easybio

Comprehensive Single-Cell Annotation and Transcriptomic Analysis
Toolkit

dprocess_dgeList function

<dl><dt>x</dt>
<dd>A <code>DGEList</code> object containing raw count data.</dd>
<dt>group.column</dt>
<dd>The name of the column in <code>x$samples</code> that contains the
grouping information for the samples.</dd>
<dt>min.count</dt>
<dd>The minimum number of counts required for a gene to be
considered expressed. Genes with counts below this threshold in any group
will be filtered out. Defaults to 10.</dd></dl>

Arguments

Filter Low-Expressed Genes and Normalize DGEList Data — dprocess_dgeList

<dl>

<dt>x</dt>
<dd>A <code>DGEList</code> object containing raw count data.</dd>


<dt>group.column</dt>
<dd>The name of the column in <code>x$samples</code> that contains the
grouping information for the samples.</dd>


<dt>min.count</dt>
<dd>The minimum number of counts required for a gene to be
considered expressed. Genes with counts below this threshold in any group
will be filtered out. Defaults to 10.</dd>

</dl>

dprocess_dgeList: Filter Low-Expressed Genes and Normalize DGEList Data

Description

Usage

Value

Arguments