prepare_tcga

This function prepares TCGA data for downstream analyses such as differential expression analysis with <code>limma</code> or survival analysis.
It extracts and processes the necessary information from the TCGA data object, separating tumor and non-tumor samples.

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

prepare_tcga function

<dl><dt>data</dt>
<dd>A <code>SummarizedExperiment</code> object containing TCGA data, typically obtained from R package <code>TCGABiolinks</code>.</dd></dl>

Arguments

Prepare TCGA Data for Analysis — prepare_tcga

<dl>

<dt>data</dt>
<dd>A <code>SummarizedExperiment</code> object containing TCGA data, typically obtained from R package <code>TCGABiolinks</code>.</dd>

</dl>

prepare_tcga: Prepare TCGA Data for Analysis

Description

Usage

Value

Arguments