limmaFit

This function fits a linear model to processed <code>DGEList</code> data using the
<code>limma</code> package. It defines contrasts between groups and performs
differential expression analysis.

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

limmaFit function

<dl><dt>x</dt>
<dd>A processed <code>DGEList</code> object containing normalized 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></dl>

Arguments

Fit a Linear Model for RNA-seq data using limma — limmaFit

<dl>

<dt>x</dt>
<dd>A processed <code>DGEList</code> object containing normalized 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>

</dl>

limmaFit: Fit a Linear Model for RNA-seq data using limma

Description

Usage

Value

Arguments