To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

diffHic

DOI: 10.18129/B9.bioc.diffHic    

Differential Analyis of Hi-C Data

Bioconductor version: Release (3.6)

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>

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

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 1.10.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License GPL-3
Depends R (>= 3.4), 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, zlibbioc, Rcpp
Suggests BSgenome.Ecoli.NCBI.20080805, Matrix
SystemRequirements C++11
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package diffHic_1.10.0.tar.gz
Windows Binary diffHic_1.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) diffHic_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/diffHic
Package Short Url http://bioconductor.org/packages/diffHic/
Package Downloads Report Download Stats

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