csdR

Differential gene co-expression

Bioconductor version: 3.23 · Package version: 1.18.0

This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford's algorithm.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("csdR")

Details

Maintainer	Jakob Peder Pettersen <jakobpeder.pettersen@gmail.com>
Author	Jakob Peder Pettersen [aut, cre] (ORCID: <https://orcid.org/0000-0002-3485-1634>)
License	GPL-3
URL	https://almaaslab.github.io/csdR, https://github.com/AlmaasLab/csdR
Bug Reports	https://github.com/AlmaasLab/csdR/issues
Downloads rank	312
Source branch	RELEASE_3_23
biocViews	DifferentialExpression, GeneExpression, GraphAndNetwork, Network, Software

Documentation

Analyzing differential co-expression with csdR

Download

Follow the installation instructions to use this package in your R session.

Source package	csdR_1.18.0.tar.gz
Windows binary (x86_64)	csdR_1.17.0.zip
macOS binary (arm64)	csdR_1.18.0.tgz
macOS binary (x86_64)	csdR_1.18.0.tgz

Dependencies

Depends: R (>= 4.1.0)

Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp

LinkingTo: Rcpp

Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr