diffHic

DOI: 10.18129/B9.bioc.diffHic    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see diffHic.

Differential Analyis of Hi-C Data

Bioconductor version: 3.9

Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.

Author: Aaron Lun [aut, cre], Gordon Smyth [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("diffHic")

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("diffHic")

 

PDF		diffHic Vignette
PDF		diffHicUsersGuide.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software
Version	1.16.0
In Bioconductor since	BioC 3.1 (R-3.2) (4.5 years)
License	GPL-3
Depends	R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment
Imports	Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer
LinkingTo	Rhtslib(>= 1.13.1), zlibbioc, Rcpp
Suggests	BSgenome.Ecoli.NCBI.20080805, Matrix, testthat
SystemRequirements	C++11
Enhances
URL
Depends On Me
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Build Report

Package Archives

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

Source Package	diffHic_1.16.0.tar.gz
Windows Binary	diffHic_1.16.0.zip
Mac OS X 10.11 (El Capitan)	diffHic_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/diffHic
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/diffHic
Package Short Url	https://bioconductor.org/packages/diffHic/
Package Downloads Report	Download Stats