csdR
This is the development version of csdR; for the stable release version, see csdR.
Differential gene co-expression
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Jakob Peder Pettersen <jakobpeder.pettersen at gmail.com>
citation("csdR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("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")| csdR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, Network, Software |
| Version | 1.13.3 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | csdR_1.13.3.tar.gz |
| Windows Binary (x86_64) | csdR_1.13.3.zip |
| macOS Binary (x86_64) | csdR_1.13.3.tgz |
| macOS Binary (arm64) | csdR_1.13.3.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 |