SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
  install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to ‘xbioc’ could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be posted on the issues section or emailed to: meichen@live.unc.edu