CDSeqR: fast complete deconvolution for gene expression data from bulk tissues.

ABSTRACT:

Background

Biological tissues consist of heterogenous populations of cells. Because gene expression patterns from bulk tissue samples reflect the contributions from all cells in the tissue, understanding the contribution of individual cell types to the overall gene expression in the tissue is fundamentally important. We recently developed a computational method, CDSeq, that can simultaneously estimate both sample-specific cell-type proportions and cell-type-specific gene expression profiles using only bulk RNA-Seq counts from multiple samples. Here we present an R implementation of CDSeq (CDSeqR) with significant performance improvement over the original implementation in MATLAB and an added new function to aid cell type annotation. The R package would be of interest for the broade

SUBMITTER: Kang K 

PROVIDER: S-EPMC8142515 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature