TumorDecon: A digital cytometry software

SoftwareX. 2022 Jun;18:101072. doi: 10.1016/j.softx.2022.101072. Epub 2022 Apr 7.

Abstract

There are many experimental methods for characterizing immune profiles of tumors, such as flow and mass cytometry. However, these approaches are time and resource intensive. Thus, several "digital cytometry" methods have been developed to extract cell frequencies from RNA-seq data. Here, we introduce TumorDecon, named for its potential to deconvolve the distribution of cells from the gene expression levels of a bulk of cells, such as a tumor. The Python package provides an accessible way of applying these methods. It includes four deconvolution methods as well as several gene sets, signature matrices, and functions for generating custom signature matrices.

Keywords: CIBERSORT; DeconRNASeq; Deconvolution methods; Digital cytometry; Signature matrix; SingScore; ssGSEA.