bnbc

This is the released version of bnbc; for the devel version, see bnbc.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Bandwise normalization and batch correction of Hi-C data

Bioconductor version: Release (3.23)

Tools to normalize (several) Hi-C data from replicates.

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

Maintainer: Kipper Fletez-Brant <cafletezbrant at gmail.com>

Citation (from within R, enter citation("bnbc")):

Kipper Fletez-Brant, Kasper Daniel Hansen. bnbc: Bandwise normalization and batch correction of Hi-C data. doi:10.18129/B9.bioc.bnbc, R package version 1.34.0, https://bioconductor.org/packages/bnbc.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("bnbc")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("bnbc")

bnbc User's Guide	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	HiC, Normalization, Preprocessing, Software
Version	1.34.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges
Imports	Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, Seqinfo, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils
System Requirements
URL	https://github.com/hansenlab/bnbc
Bug Reports	https://github.com/hansenlab/bnbc/issues

Suggests	BiocStyle, knitr, rmarkdown, RUnit, BSgenome.Hsapiens.UCSC.hg19
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	bnbc_1.34.0.tar.gz
Windows Binary (x86_64)	bnbc_1.34.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	bnbc_1.34.0.tgz
macOS Binary (sonoma-arm64)	bnbc_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bnbc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bnbc
Package Short Url	https://bioconductor.org/packages/bnbc/
Package Downloads Report	Download Stats