tuneParameters

This function tunes the <code>resolution</code> parameter in <code>Seurat::FindClusters()</code> and the number of top differential genes (<code>N</code>) to obtain different cell type annotation results. The function generates UMAP plots for each parameter combination, allowing for a comparison of how different settings affect the clustering and annotation.

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

tuneParameters function

<dl><dt>srt</dt>
<dd>Seurat object, the input data object to be analyzed.</dd>
<dt>resolution</dt>
<dd>numeric vector, a vector of resolution values to be tested in <code>Seurat::FindClusters()</code>.</dd>
<dt>N</dt>
<dd>integer vector, a vector of values indicating the number of top differential genes to be used for matching in <code>matchCellMarker2()</code>.</dd>
<dt>spc</dt>
<dd>character, the species parameter for the <code>matchCellMarker2()</code> function, specifying the organism.</dd></dl>

Arguments

Optimize Resolution and Gene Number Parameters for Cell Type Annotation — tuneParameters

<dl>

<dt>srt</dt>
<dd>Seurat object, the input data object to be analyzed.</dd>


<dt>resolution</dt>
<dd>numeric vector, a vector of resolution values to be tested in <code>Seurat::FindClusters()</code>.</dd>


<dt>N</dt>
<dd>integer vector, a vector of values indicating the number of top differential genes to be used for matching in <code>matchCellMarker2()</code>.</dd>


<dt>spc</dt>
<dd>character, the species parameter for the <code>matchCellMarker2()</code> function, specifying the organism.</dd>

</dl>

tuneParameters: Optimize Resolution and Gene Number Parameters for Cell Type Annotation

Description

Usage

Value

Arguments