Package: csdR 1.11.0
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_1.11.0.tar.gz
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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
- normal_expression - Sample expression matrices for CSD
- sick_expression - Sample expression matrices for CSD
On BioConductor:csdR-1.11.0(bioc 3.20)csdR-1.10.0(bioc 3.19)
Last updated 2 months agofrom:14407273b7
Exports:partial_argsortrun_cor_bootstraprun_csd
Dependencies:AnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdoParalleldynamicTreeCutevaluatefansifarverfastclusterfastmapfontawesomeforeachforeignFormulafsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.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 |