Introduction | Citing bnbc | Terminology | Dependencies | The ContactGroup class from bnbc | Alternatives | Getting your data into bnbc | Getting your data out of *.cooler files | Working with bnbc contact matrices | Per-Sample Adjustments | Cross Sample Normalization | sessionInfo() | References
Package: bnbc 1.35.0
Kipper Fletez-Brant
bnbc: Bandwise normalization and batch correction of Hi-C data
Tools to normalize (several) Hi-C data from replicates.
Authors:
bnbc_1.35.0.tar.gz
bnbc_1.35.0.zip(r-4.7-x86_64)bnbc_1.35.0.zip(r-4.7-arm64)bnbc_1.35.0.zip(r-4.6-x86_64)bnbc_1.35.0.zip(r-4.6-arm64)bnbc_1.35.0.zip(r-4.5-x86_64)
bnbc_1.35.0.tgz(r-4.6-x86_64)bnbc_1.35.0.tgz(r-4.6-arm64)bnbc_1.35.0.tgz(r-4.5-x86_64)bnbc_1.35.0.tgz(r-4.5-arm64)
bnbc_1.35.0.tar.gz(r-4.7-arm64)bnbc_1.35.0.tar.gz(r-4.7-x86_64)bnbc_1.35.0.tar.gz(r-4.6-arm64)bnbc_1.35.0.tar.gz(r-4.6-x86_64)
bnbc_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bnbc/json (API)
| # 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
Datasets:
- cgEx - Sample chr22 Data
On BioConductor:bnbc-1.35.0(bioc 3.24)bnbc-1.34.0(bioc 3.23)
hicpreprocessingnormalizationsoftwarecpp
Last updated from:3d959e0ddf. Checks:1 WARNING, 15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 248 | ||
| linux-devel-arm64 | OK | 351 | ||
| linux-devel-x86_64 | OK | 508 | ||
| source / vignettes | OK | 358 | ||
| linux-release-arm64 | OK | 362 | ||
| linux-release-x86_64 | OK | 392 | ||
| macos-release-arm64 | OK | 401 | ||
| macos-release-x86_64 | OK | 575 | ||
| macos-oldrel-arm64 | OK | 231 | ||
| macos-oldrel-x86_64 | OK | 711 | ||
| windows-devel-arm64 | OK | 458 | ||
| windows-devel-x86_64 | OK | 622 | ||
| windows-release-arm64 | OK | 399 | ||
| windows-release-x86_64 | OK | 571 | ||
| windows-oldrel-x86_64 | OK | 577 | ||
| wasm-release | OK | 203 |
Exports:bandband<-bnbcboxSmoothercg2bedgraph2cgApplycgBandApplycolDatacolData<-ContactGroupcontactscontacts<-distanceIdxdropGroupZerosgaussSmoothergetBandIdxgetBandMatrixgetChrCGFromCoolsgetChrIdxgetGroupZeroslibrarySizelogCPMrowDatarowData<-show
Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocParallelBiostringsbitbit64bitopsblobbslibcachemclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydigestdir.expiryEBImageedgeRevaluatefastmapfftwtoolsfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenefiltergenericsGenomicRangesgluehighrhtmltoolshtmlwidgetshttrIRangesjpegjquerylibjsonliteKEGGRESTknitrlambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpkgconfigpngpreprocessCoreR6rappdirsRcppRCurlrhdf5rhdf5filtersRhdf5librlangrmarkdownRSQLiteS4ArraysS4VectorssassSeqinfosnowSparseArraystatmodSummarizedExperimentsurvivalsvasystifftinytexvctrsxfunXMLxtableXVectoryaml
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 |
