csdR

DOI: 10.18129/B9.bioc.csdR    

This is the development version of csdR; to use it, please install the devel version of Bioconductor.

Differential gene co-expression

Bioconductor version: Development (3.14)

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 "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.8
In Bioconductor since BioC 3.14 (R-4.1)
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_0.99.8.tar.gz
Windows Binary csdR_0.99.8.zip (32- & 64-bit)
macOS 10.13 (High Sierra) csdR_0.99.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/csdR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/csdR
Package Short Url https://bioconductor.org/packages/csdR/
Package Downloads Report Download Stats

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