TumorDecon

TumorDecon is an open source Python package, which includes four deconvolution methods (DeconRNAseq [Gong2013], CIBERSORT [Newman2015], ssGSEA [Şenbabaoğlu2016], Singscore [Foroutan2018]) and several cell signature matrixes, including LM22.

The input of this software is the gene expression profile of the tumor, and the output is the relative number of each cell type.

Users have an option to choose any of the implemented deconvolution methods and included signature matrixes or import their own signature matrix to get the results.

Supported by NCI ITCR program and UMass Amherst.

If you use the package or some parts of codes please cite:

Rachel A. Aronow, Shaya Akbarinejad, Trang Le, Sumeyye Su, Leili Shahriyari, TumorDecon: A digital cytometry software, SoftwareX, Volume 18, 2022, 101072, https://doi.org/10.1016/j.softx.2022.101072.
T. Le, R. Aronow, A. Kirshtein, L. Shahriyari, A review of digital cytometry methods: estimating the relative abundance of cell types in a bulk of cells, Briefing in Bioinformatics, 2020.