Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA

Yang Liu, Lin Yang, Yi Zhang, Jin Wang, Jennifer Altreuter, Aashna Jhaveri, Cheryl J. Wong, Li Song, Jingxin Fu, Len Taing, Sudheshna Bodapati, Avinash Sahu, Collin Tokheim, Zexian Zeng, Gali Bai, Ming Tang, Xintao Qiu, Henry W. Long, Franziska Michor, X. Shirley Liu

Published: 2023-06-29 DOI: 10.1038/s41596-023-00841-8

RNA-seq

Tumor immunity

Computational analysis

RIMA

Immunotherapy

AI 解读

Deoxyfluorination of phenols for chemoselective18F-labeling of peptides

Stable isotope tracing to assess tumor metabolism in vivo

Measuring DNA modifications with the comet assay: a compendium of protocols

Detect-seq, a chemical labeling and biotin pull-down approach for the unbiased and genome-wide off-target evaluation of programmable cytosine base editors

A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome

Spooling electrochemiluminescence spectroscopy: development, applications and beyond

Chronic, cortex-wide imaging of specific cell populations during behavior

Chromatin accessibility profiling by ATAC-seq

Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture

Pooled genetic perturbation screens with image-based phenotypes

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Sections

Figures

References

Read alignment and quality control
Gene quantification
Batch effect removal
Differential expression and gene set enrichment
Cell infiltration estimation
Immunotherapy response prediction
Immune repertoire inference
Tumor mutation detection and characterization of the mutational landscape
Neoantigen prediction
Microbiota classification and quantification
RIMA pipeline implementation
Outlook
Conclusion
Acknowledgements

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Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA

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