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("phyloseq")

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.