Package: csdR 1.13.3
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_1.13.3.tar.gz
csdR_1.13.3.zip(r-4.5)csdR_1.13.3.zip(r-4.4)csdR_1.13.3.zip(r-4.3)
csdR_1.13.3.tgz(r-4.4-x86_64)csdR_1.13.3.tgz(r-4.4-arm64)csdR_1.13.3.tgz(r-4.3-x86_64)csdR_1.13.3.tgz(r-4.3-arm64)
csdR_1.13.3.tar.gz(r-4.5-noble)csdR_1.13.3.tar.gz(r-4.4-noble)
csdR_1.13.3.tgz(r-4.4-emscripten)csdR_1.13.3.tgz(r-4.3-emscripten)
csdR.pdf |csdR.html✨
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:https://almaaslab.github.io
- normal_expression - Sample expression matrices for CSD
- sick_expression - Sample expression matrices for CSD
On BioConductor:csdR-1.13.3(bioc 3.21)csdR-1.12.0(bioc 3.20)
differentialexpressiongraphandnetworkgeneexpressionnetworkcppopenmp
Last updated 1 months agofrom:0df2dbcd14. Checks:OK: 6 ERROR: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 08 2024 |
| R-4.5-win-x86_64 | ERROR | Dec 08 2024 |
| R-4.5-linux-x86_64 | OK | Dec 08 2024 |
| R-4.4-win-x86_64 | OK | Dec 08 2024 |
| R-4.4-mac-x86_64 | OK | Dec 08 2024 |
| R-4.4-mac-aarch64 | OK | Dec 08 2024 |
| R-4.3-win-x86_64 | ERROR | Dec 08 2024 |
| R-4.3-mac-x86_64 | ERROR | Dec 08 2024 |
| R-4.3-mac-aarch64 | OK | Dec 08 2024 |
Exports:partial_argsortrun_cor_bootstraprun_csd
Dependencies:AnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdoParalleldynamicTreeCutevaluatefansifarverfastclusterfastmapfontawesomeforeachforeignFormulafsgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngpreprocessCoreR6rappdirsRColorBrewerRcppRhpcBLASctlrlangrmarkdownrpartRSQLiterstudioapiS4VectorssassscalesstringistringrsurvivalsystibbletinytexUCSC.utilsutf8vctrsviridisviridisLiteWGCNAwithrxfunXVectoryamlzlibbioc
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 |
