dgeList

This function creates a <code>DGEList</code> object from a count matrix, sample
information, and feature information. It is designed to facilitate the
analysis of differential gene expression using the edgeR package.

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

dgeList function

<dl><dt>count</dt>
<dd>A numeric matrix where rows represent features (e.g., genes) and
columns represent samples. Row names should correspond to feature identifiers,
and column names should correspond to sample identifiers.</dd>
<dt>sample.info</dt>
<dd>A data frame containing information about the samples. The
number of rows should match the number of columns in the <code>count</code> matrix.</dd>
<dt>feature.info</dt>
<dd>A data frame containing information about the features. The
number of rows should match the number of rows in the <code>count</code> matrix.</dd></dl>

Arguments

Construct a DGEList Object — dgeList

<dl>

<dt>count</dt>
<dd>A numeric matrix where rows represent features (e.g., genes) and
columns represent samples. Row names should correspond to feature identifiers,
and column names should correspond to sample identifiers.</dd>


<dt>sample.info</dt>
<dd>A data frame containing information about the samples. The
number of rows should match the number of columns in the <code>count</code> matrix.</dd>


<dt>feature.info</dt>
<dd>A data frame containing information about the features. The
number of rows should match the number of rows in the <code>count</code> matrix.</dd>

</dl>

dgeList: Construct a DGEList Object

Description

Usage

Value

Arguments