When and why to use this package | Installation | Some theoretical considerations | Workflow outline | How to we approach from here? | Considerations to note | Number of bootstrap iterations | Number of threads | Memory consumption | Number of top gene pairs to pick | Session info for this vignette | References
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
csdR/json (API)
| # 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
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)
differentialexpressiongraphandnetworkgeneexpressionnetworkcppopenmp
Last updated from:9e450b5723. Checks:1 WARNING, 10 OK, 3 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 202 | ||
| linux-devel-arm64 | OK | 205 | ||
| linux-devel-x86_64 | OK | 281 | ||
| source / vignettes | OK | 234 | ||
| linux-release-arm64 | OK | 225 | ||
| linux-release-x86_64 | OK | 256 | ||
| macos-release-arm64 | OK | 199 | ||
| macos-release-x86_64 | OK | 450 | ||
| macos-oldrel-arm64 | OK | 183 | ||
| macos-oldrel-x86_64 | OK | 357 | ||
| windows-devel | ERROR | 236 | ||
| windows-release | ERROR | 216 | ||
| windows-oldrel | ERROR | 231 | ||
| wasm-release | OK | 193 |
Exports:partial_argsortrun_cor_bootstraprun_csd
Dependencies:backportsbase64encbslibcachemcheckmatecliclustercodetoolscolorspacecpp11data.tabledigestdoParalleldynamicTreeCutevaluatefarverfastclusterfastmapfontawesomeforeachforeignFormulafsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsimputeisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMatrixmatrixStatsmemoisemimennetpreprocessCoreR6rappdirsRColorBrewerRcppRhpcBLASctlrlangrmarkdownrpartrstudioapiS7sassscalesstringistringrsurvivaltinytexvctrsviridisLiteWGCNAwithrxfunyaml
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 |
