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csdR

Differential gene co-expression


Bioconductor version: Release (3.18)

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 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1.0)
Imports WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
System Requirements
URL https://almaaslab.github.io/csdR https://github.com/AlmaasLab/csdR
Bug Reports https://github.com/AlmaasLab/csdR/issues
See More
Suggests rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr
Linking To Rcpp
Enhances
Depends On Me
Imports Me
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Links To Me
Build Report Build Report

Package Archives

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

Source Package csdR_1.8.0.tar.gz
Windows Binary
macOS Binary (x86_64) csdR_1.8.0.tgz
macOS Binary (arm64) csdR_1.8.0.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