diffHic

DOI: 10.18129/B9.bioc.diffHic    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see diffHic.

Differential Analyis of Hi-C Data

Bioconductor version: 3.7

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 <alun at wehi.edu.au>

Maintainer: Aaron Lun <alun at wehi.edu.au>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("diffHic")

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	1.12.1
In Bioconductor since	BioC 3.1 (R-3.2) (3.5 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
LinkingTo	Rhtslib(>= 1.12.1), zlibbioc, Rcpp
Suggests	BSgenome.Ecoli.NCBI.20080805, Matrix
SystemRequirements	C++11
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	diffHic_1.12.1.tar.gz
Windows Binary	diffHic_1.12.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	diffHic_1.12.1.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	http://bioconductor.org/packages/diffHic/
Package Downloads Report	Download Stats