GitHub - AlmaasLab/csdR: Efficient CSD implementation in R (original) (raw)

csdR

This R-package implements the CSD algorithm presented by Voigt et al. 2017 in an efficient manner.

• Requrirements: Requirements: R (version 4.1.0 or higher) with packages WGCNA, optparse, glue, magrittr and Rcpp (and of course a C++ compiler) installed. Additionally, having an optimized Blas library such as openBlas is highly recommended for performance reasons (see this link for more info).

Installation

In order to install the release version from Bioconductor, do type in the R terminal:

if(!requireNamespace("BiocManager")){
  install.packages("BiocManager")
}
BiocManager::install("csdR")

If you want to install the development version instead:

# install.packages("devtools")
devtools::install_github("AlmaasLab/csdR", ref = "main")

Usage

Please see the package vignette. Additionally check out the article on csdR:

Pettersen, J.P., Almaas, E. csdR, an R package for differential co-expression analysis. BMC Bioinformatics 23, 79 (2022). https://doi.org/10.1186/s12859-022-04605-1

Issues and feedback

Please use the repository's issue tracker if you cannot make the package work or if you have suggestions for improvements.