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

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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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