matchCellMarker2

This function matches markers from the <code>FindAllMarkers</code> output with the
<code>cellMarker2</code> dataset, filtering by species and selecting the top genes based
on their average log2 fold change and adjusted p-values.

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

matchCellMarker2 function

<dl><dt>marker</dt>
<dd>A data frame of markers obtained from the <code>FindAllMarkers</code>
function, expected to contain columns such as <code>avg_log2FC</code>, <code>p_val_adj</code>,
and <code>gene</code>.</dd>
<dt>n</dt>
<dd>An integer specifying the top number of genes to match from the
input markers.</dd>
<dt>spc</dt>
<dd>A character string specifying the species, which can be either
'Human' or 'Mouse'.</dd></dl>

Arguments

Match Markers with cellMarker2 Dataset — matchCellMarker2

<dl>

<dt>marker</dt>
<dd>A data frame of markers obtained from the <code>FindAllMarkers</code>
function, expected to contain columns such as <code>avg_log2FC</code>, <code>p_val_adj</code>,
and <code>gene</code>.</dd>


<dt>n</dt>
<dd>An integer specifying the top number of genes to match from the
input markers.</dd>


<dt>spc</dt>
<dd>A character string specifying the species, which can be either
'Human' or 'Mouse'.</dd>

</dl>

matchCellMarker2: Match Markers with cellMarker2 Dataset

Description

Usage

Value

Arguments

Examples