csdR

Differential gene co-expression

Bioconductor version: Release (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>

Citation (from within R, enter citation("csdR")):

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")

csdR	HTML	R Script
Reference Manual	PDF
NEWS	Text

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
Linking To	Rcpp
Suggests	rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr
System Requirements
Enhances
URL	https://almaaslab.github.io/csdR https://github.com/AlmaasLab/csdR
Bug Reports	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