Package: csdR 1.19.0

Jakob Peder Pettersen

csdR: Differential gene co-expression

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.

Authors:Jakob Peder Pettersen [aut, cre]

csdR_1.19.0.tar.gz
csdR_1.19.0.zip(r-4.7)csdR_1.19.0.zip(r-4.6)csdR_1.19.0.zip(r-4.5)
csdR_1.19.0.tgz(r-4.6-x86_64)csdR_1.19.0.tgz(r-4.6-arm64)csdR_1.19.0.tgz(r-4.5-x86_64)csdR_1.19.0.tgz(r-4.5-arm64)
csdR_1.19.0.tar.gz(r-4.7-arm64)csdR_1.19.0.tar.gz(r-4.7-x86_64)csdR_1.19.0.tar.gz(r-4.6-arm64)csdR_1.19.0.tar.gz(r-4.6-x86_64)
csdR_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
csdR/json (API)
NEWS

# Install 'csdR' in R:

install.packages('csdR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/almaaslab/csdr/issues

Pkgdown/docs site:https://almaaslab.github.io

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

normal_expression - Sample expression matrices for CSD
sick_expression - Sample expression matrices for CSD

On BioConductor:csdR-1.19.0(bioc 3.24)csdR-1.18.0(bioc 3.23)

differentialexpression graphandnetwork geneexpression network cpp openmp

5.32 score 7 stars 6 scripts 292 downloads 3 exports 70 dependencies

Last updated from:9e450b5723. Checks:1 WARNING, 10 OK, 3 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	188
linux-devel-arm64	OK	194
linux-devel-x86_64	OK	217
source / vignettes	OK	250
linux-release-arm64	OK	226
linux-release-x86_64	OK	272
macos-release-arm64	OK	234
macos-release-x86_64	OK	361
macos-oldrel-arm64	OK	264
macos-oldrel-x86_64	OK	383
windows-devel	ERROR	243
windows-release	ERROR	230
windows-oldrel	ERROR	209
wasm-release	OK	154

Exports:partial_argsort run_cor_bootstrap run_csd

Dependencies:backports base64enc bslib cachem checkmate cli cluster codetools colorspace cpp11 data.table digest doParallel dynamicTreeCut evaluate farver fastcluster fastmap fontawesome foreach foreign Formula fs ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets impute isoband iterators jquerylib jsonlite knitr labeling lattice lifecycle magrittr Matrix matrixStats memoise mime nnet preprocessCore R6 rappdirs RColorBrewer Rcpp RhpcBLASctl rlang rmarkdown rpart rstudioapi S7 sass scales stringi stringr survival tinytex vctrs viridisLite WGCNA withr xfun yaml

Analyzing differential co-expression with csdR

Rendered fromcsdR.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2024-11-07
Started: 2021-06-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Sample expression matrices for CSD	data-expression normal_expression sick_expression
Extract indecies corresponding to the largest elements	partial_argsort
Run bootstrapping of Spearman correlations within a dataset	run_cor_bootstrap
Run CSD analysis	run_csd