TimiGP: An R Package to Depict the Tumor Microenvironment from Bulk Transcriptomics

Authors

Chenyang Li
Jianjun Zhang
Chao Cheng

Language

English

Publication Date

12-15-2023

Journal

STAR Protocols

DOI

10.1016/j.xpro.2023.102742

PMID

38019649

PMCID

PMC10698325

PubMedCentral® Posted Date

11-27-2023

PubMedCentral® Full Text Version

Post-Print

Abstract

Exploring the clinical relevance of diverse immune cell types within the tumor microenvironment is pivotal for unraveling cancer intricacies and developing treatments. Here, we present a protocol for using tumor immune microenvironment illustration based on gene pairs, an R package to deduce cell-cell interactions, unveiling the association between immune cell relative abundance and patient prognoses from bulk gene expression and survival data. We describe steps for harnessing cell-type markers derived from single-cell RNA sequencing data to map the tumor immune microenvironment across a spectrum of cancer types. For complete details on the use and execution of this protocol, please refer to Li et al. (2023).

Keywords

Humans, Tumor Microenvironment, Gene Expression Profiling, Cell Communication, Neoplasms, Bioinformatics, Single Cell, Cancer, Genomics, RNA-seq, Immunology, Gene Expression, Systems biology

Published Open-Access

yes

Recommended Citation

Chenyang Li, Jianjun Zhang, and Chao Cheng, "TimiGP: An R Package to Depict the Tumor Microenvironment from Bulk Transcriptomics" (2023). Faculty and Staff Publications. 1195.
https://digitalcommons.library.tmc.edu/baylor_docs/1195