CIBERSORT

CIBERSORT, also called CIBERSORTx, is a bioinformatics tool used to deconvolute cell type proportions and gene expression profiles from bulk RNA sequencing datasets.^[1]^[2]^[3]^[4] It is among the fastest growing software tools in the life sciences.^[5]

References

^ Newman, Aaron M.; Liu, Chih Long; Green, Michael R.; Gentles, Andrew J.; Feng, Weiguo; Xu, Yue; Hoang, Chuong D.; Diehn, Maximilian; Alizadeh, Ash A. (2015). "Robust enumeration of cell subsets from tissue expression profiles". Nature Methods. 12 (5): 453–457. doi:10.1038/nmeth.3337. ISSN 1548-7105. PMC 4739640.
^ Newman, Aaron M.; Steen, Chloé B.; Liu, Chih Long; Gentles, Andrew J.; Chaudhuri, Aadel A.; Scherer, Florian; Khodadoust, Michael S.; Esfahani, Mohammad S.; Luca, Bogdan A.; Steiner, David; Diehn, Maximilian; Alizadeh, Ash A. (2019). "Determining cell type abundance and expression from bulk tissues with digital cytometry". Nature Biotechnology. 37 (7): 773–782. doi:10.1038/s41587-019-0114-2. ISSN 1546-1696. PMC 6610714.
^ Chen, Binbin; Khodadoust, Michael S.; Liu, Chih Long; Newman, Aaron M.; Alizadeh, Ash A. (2018), von Stechow, Louise (ed.), "Profiling Tumor Infiltrating Immune Cells with CIBERSORT", Cancer Systems Biology, vol. 1711, New York, NY: Springer New York, pp. 243–259, doi:10.1007/978-1-4939-7493-1_12, ISBN 978-1-4939-7492-4, PMC 5895181, PMID 29344893, retrieved 2023-02-01
^ Steen, Chloé B.; Liu, Chih Long; Alizadeh, Ash A.; Newman, Aaron M. (2020), Kidder, Benjamin L. (ed.), "Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx", Stem Cell Transcriptional Networks: Methods and Protocols, New York, NY: Springer US, pp. 135–157, doi:10.1007/978-1-0716-0301-7_7, ISBN 978-1-0716-0301-7, PMC 7695353, PMID 31960376, retrieved 2023-02-08
^ Hutson, Matthew (2023-01-12). "Hunting for the best bioscience software tool? Check this database". Nature. doi:10.1038/d41586-023-00053-w.

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[1] Newman, Aaron M.; Liu, Chih Long; Green, Michael R.; Gentles, Andrew J.; Feng, Weiguo; Xu, Yue; Hoang, Chuong D.; Diehn, Maximilian; Alizadeh, Ash A. (2015). "Robust enumeration of cell subsets from tissue expression profiles". Nature Methods. 12 (5): 453–457. doi:10.1038/nmeth.3337. ISSN 1548-7105. PMC 4739640.

[2] Newman, Aaron M.; Steen, Chloé B.; Liu, Chih Long; Gentles, Andrew J.; Chaudhuri, Aadel A.; Scherer, Florian; Khodadoust, Michael S.; Esfahani, Mohammad S.; Luca, Bogdan A.; Steiner, David; Diehn, Maximilian; Alizadeh, Ash A. (2019). "Determining cell type abundance and expression from bulk tissues with digital cytometry". Nature Biotechnology. 37 (7): 773–782. doi:10.1038/s41587-019-0114-2. ISSN 1546-1696. PMC 6610714.

[3] Chen, Binbin; Khodadoust, Michael S.; Liu, Chih Long; Newman, Aaron M.; Alizadeh, Ash A. (2018), von Stechow, Louise (ed.), "Profiling Tumor Infiltrating Immune Cells with CIBERSORT", Cancer Systems Biology, vol. 1711, New York, NY: Springer New York, pp. 243–259, doi:10.1007/978-1-4939-7493-1_12, ISBN 978-1-4939-7492-4, PMC 5895181, PMID 29344893, retrieved 2023-02-01

[4] Steen, Chloé B.; Liu, Chih Long; Alizadeh, Ash A.; Newman, Aaron M. (2020), Kidder, Benjamin L. (ed.), "Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx", Stem Cell Transcriptional Networks: Methods and Protocols, New York, NY: Springer US, pp. 135–157, doi:10.1007/978-1-0716-0301-7_7, ISBN 978-1-0716-0301-7, PMC 7695353, PMID 31960376, retrieved 2023-02-08

[5] Hutson, Matthew (2023-01-12). "Hunting for the best bioscience software tool? Check this database". Nature. doi:10.1038/d41586-023-00053-w.

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CIBERSORT

References

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