csdR
Differential gene co-expression
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("csdR")Details
| Maintainer | Jakob Peder Pettersen <jakobpeder.pettersen@gmail.com> |
| Author | Jakob Peder Pettersen [aut, cre] (ORCID: <https://orcid.org/0000-0002-3485-1634>) |
| License | GPL-3 |
| URL | https://almaaslab.github.io/csdR, https://github.com/AlmaasLab/csdR |
| Bug Reports | https://github.com/AlmaasLab/csdR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, Network, Software |
| Package Short Url | https://bioconductor.org/packages/csdR/ |
Citation
From within R, enter citation("csdR"):
Jakob Peder Pettersen. csdR: Differential gene co-expression. doi:10.18129/B9.bioc.csdR, R package version 1.18.0, https://bioconductor.org/packages/csdR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | csdR_1.18.0.tar.gz |
| Windows binary (x86_64) | csdR_1.17.0.zip |
| macOS binary (arm64) | csdR_1.18.0.tgz |
| macOS binary (x86_64) | csdR_1.18.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
LinkingTo: Rcpp
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr