Package: bnbc 1.27.0
bnbc: Bandwise normalization and batch correction of Hi-C data
Tools to normalize (several) Hi-C data from replicates.
Authors:
bnbc_1.27.0.tar.gz
bnbc_1.27.0.zip(r-4.5)bnbc_1.27.0.zip(r-4.4)bnbc_1.27.0.zip(r-4.3)
bnbc_1.27.0.tgz(r-4.4-arm64)bnbc_1.27.0.tgz(r-4.4-x86_64)bnbc_1.27.0.tgz(r-4.3-arm64)bnbc_1.27.0.tgz(r-4.3-x86_64)
bnbc_1.27.0.tar.gz(r-4.5-noble)bnbc_1.27.0.tar.gz(r-4.4-noble)
bnbc_1.27.0.tgz(r-4.4-emscripten)bnbc_1.27.0.tgz(r-4.3-emscripten)
bnbc.pdf |bnbc.html✨
bnbc/json (API)
NEWS
# Install 'bnbc' in R: |
install.packages('bnbc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hansenlab/bnbc/issues
- cgEx - Sample chr22 Data
On BioConductor:bnbc-1.27.0(bioc 3.20)bnbc-1.26.0(bioc 3.19)
Last updated 2 months agofrom:89c087e8e6
Exports:bandband<-bnbcboxSmoothercg2bedgraph2cgApplycgBandApplycolDatacolData<-ContactGroupcontactscontacts<-distanceIdxdropGroupZerosgaussSmoothergetBandIdxgetBandMatrixgetChrCGFromCoolsgetChrIdxgetGroupZeroslibrarySizelogCPMrowDatarowData<-show
Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbslibcachemclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydigestEBImageedgeRevaluatefansifarverfastmapfftwtoolsfontawesomeformatRfsfutile.loggerfutile.optionsgenefilterGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtableHiCBrickshighrhmshtmltoolshtmlwidgetshttrIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogressR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrreshape2rhdf5rhdf5filtersRhdf5librlangrmarkdownRSQLiteS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyselecttifftinytextzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Bandwise normalization and batch correction of Hi-C data | bnbc-package |
Get Band | band band<- |
Normalize Contact Matrices with BNBC | bnbc |
Apply-type methods | cgApply cgBandApply |
Sample chr22 Data | cgEx |
Class '"ContactGroup"' | colData,ContactGroup-method colData<-,ContactGroup,DataFrame-method ContactGroup ContactGroup-class contacts contacts<- dim,ContactGroup-method distanceIdx librarySize logCPM rowData,ContactGroup-method rowData<-,ContactGroup-method show,ContactGroup-method [,ContactGroup,ANY,ANY,ANY-method |
Methods for manipulating cooler files | cg2bedgraph2 getChrCGFromCools getChrIdx getGenomeIdx |
Get Band Indices | getBandIdx |
Get Band Matrix | getBandMatrix |
Group Zero Operations | dropGroupZeros getGroupZeros |
Smoothing Operations | boxSmoother gaussSmoother |