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:Kipper Fletez-Brant [cre, aut], Kasper Daniel Hansen [aut]

bnbc_1.35.0.tar.gz
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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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

cgEx - Sample chr22 Data

On BioConductor:bnbc-1.35.0(bioc 3.24)bnbc-1.34.0(bioc 3.23)

hic preprocessing normalization software cpp

5.48 score 2 stars 15 scripts 1 mentions 25 exports 97 dependencies

Last updated from:3d959e0ddf. Checks:1 WARNING, 13 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	WARNING	272
linux-devel-arm64	OK	361
linux-devel-x86_64	OK	478
source / vignettes	OK	354
linux-release-arm64	OK	362
linux-release-x86_64	OK	433
macos-release-arm64	OK	362
macos-release-x86_64	OK	669
macos-oldrel-arm64	OK	286
macos-oldrel-x86_64	OK	752
windows-devel	OK	610
windows-release	OK	665
windows-oldrel	OK	547
wasm-release	OK	243

Exports:band band<-bnbc boxSmoother cg2bedgraph2 cgApply cgBandApply colData colData<-ContactGroup contacts contacts<-distanceIdx dropGroupZeros gaussSmoother getBandIdx getBandMatrix getChrCGFromCools getChrIdx getGroupZeros librarySize logCPM rowData rowData<-show

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics biocmake BiocParallel Biostrings bit bit64 bitops blob bslib cachem cli codetools cpp11 crayon curl data.table DBI DelayedArray digest dir.expiry EBImage edgeR evaluate fastmap fftwtools filelock fontawesome formatR fs futile.logger futile.options genefilter generics GenomicRanges glue highr htmltools htmlwidgets httr IRanges jpeg jquerylib jsonlite KEGGREST knitr lambda.r lattice lifecycle limma locfit Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl pkgconfig png preprocessCore R6 rappdirs Rcpp RCurl rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown RSQLite S4Arrays S4Vectors sass Seqinfo snow SparseArray statmod SummarizedExperiment survival sva sys tiff tinytex vctrs xfun XML xtable XVector yaml

The bnbc User's Guide

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

Rendered frombnbc.Rmdusingknitr::rmarkdown

Last update: 2026-04-26
Started: 2017-08-30

Citation

Development and contributors

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

Usage by other packages (reverse dependencies)