csdR

DOI: 10.18129/B9.bioc.csdR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see csdR.

Differential gene co-expression

Bioconductor version: 3.17

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.

Author: Jakob Peder Pettersen [aut, cre]

Maintainer: Jakob Peder Pettersen <jakobpeder.pettersen at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("csdR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("csdR")

 

HTML	R Script	csdR
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GraphAndNetwork, Network, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
LinkingTo	Rcpp
Suggests	rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr
SystemRequirements
Enhances
URL	https://almaaslab.github.io/csdR https://github.com/AlmaasLab/csdR
BugReports	https://github.com/AlmaasLab/csdR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	csdR_1.6.0.tar.gz
Windows Binary	csdR_1.5.0.zip (64-bit only)
macOS Binary (x86_64)	csdR_1.6.0.tgz
macOS Binary (arm64)	csdR_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/csdR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/csdR
Bioc Package Browser	https://code.bioconductor.org/browse/csdR/
Package Short Url	https://bioconductor.org/packages/csdR/
Package Downloads Report	Download Stats