Package: csaw 1.39.0
csaw: ChIP-Seq Analysis with Windows
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Authors:
csaw_1.39.0.tar.gz
csaw_1.39.0.zip(r-4.5)csaw_1.39.0.zip(r-4.4)csaw_1.39.0.zip(r-4.3)
csaw_1.39.0.tgz(r-4.4-x86_64)csaw_1.39.0.tgz(r-4.4-arm64)csaw_1.39.0.tgz(r-4.3-x86_64)csaw_1.39.0.tgz(r-4.3-arm64)
csaw_1.39.0.tar.gz(r-4.5-noble)csaw_1.39.0.tar.gz(r-4.4-noble)
csaw.pdf |csaw.html✨
csaw/json (API)
NEWS
# Install 'csaw' in R: |
install.packages('csaw', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:csaw-1.39.0(bioc 3.20)csaw-1.38.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:11222da7cf
Exports:asDGEListcalculateCPMcheckBimodalityclusterFDRclusterWindowsclusterWindowsListcombineOverlapscombineTestsconsolidateOverlapsconsolidateTestsconsolidateWindowscontrolClusterFDRcorrelateReadscsawUsersGuidedetailRangesempiricalFDRempiricalOverlapsextractReadsfilterWindowsfilterWindowsControlfilterWindowsGlobalfilterWindowsLocalfilterWindowsProportionfindMaximafindOverlapsListgetBestOverlapsgetBestTestgetPESizesgetWidthsmaximizeCcfmergeResultsmergeResultsListmergeWindowsmergeWindowsListminimalTestsmixedClustersmixedOverlapsmixedTestsnormFactorsnormOffsetsoverlapResultsoverlapResultsListprofileSitesreadParamreformregionCountsscaleControlFilterscaledAverageshowstrandedCountssummitOverlapsupweightSummitwindowCountswwhm
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayedgeRformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticelimmalocfitMatrixMatrixGenericsmatrixStatsmetapodmimeopensslR6RcppRhtslibRsamtoolsS4ArraysS4VectorssnowSparseArraystatmodSummarizedExperimentsysUCSC.utilsXVectorzlibbioc