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CS-CORE

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CS-CORE is a R package for cell-type-specific co-expression inference from single cell RNA-sequencing data.

Reference

Su, Chang, et al. “Cell-type-specific co-expression inference from single cell RNA-sequencing data.” Nature Communications 14.1 (2023): 4846. (https://doi.org/10.1038/s41467-023-40503-7)

Installation

CS-CORE is available on GitHub. You can install it using

## Load devtools for installing R packages from Github
library(devtools)
## Install CS-CORE from Github
install_github("ChangSuBiostats/CS-CORE")

Vignettes

  1. Get started shows an example of using CS-CORE for cell-type-specific co-expression analysis with single cell RNA-sequencing data. It includes inferring co-expressions, extracting co-expressed gene modules and functional enrichment analysis.

  2. Covariate adjustment shows how to adjust for covariates in co-expression inference with CS-CORE.

Contact us

For issues or feature requests, please visit GitHub Issues. If an issue remains unanswered for a while, you are welcome to email the maintainer at

A Python version

A Python implementation of CS-CORE is also provided here.