diffHic

This is the development version of diffHic; for the stable release version, see diffHic.

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, 3.5, 3.4, 3.3, 3.2, 3.1

Differential Analysis of Hi-C Data

Bioconductor version: Development (3.24)

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, Gordon Smyth

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>, Gordon Smyth <smyth at wehi.edu.au>, Hannah Coughlin <coughlin.h at wehi.edu.au>

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

Aaron Lun, Gordon Smyth. diffHic: Differential Analysis of Hi-C Data. doi:10.18129/B9.bioc.diffHic, R package version 1.45.0, https://bioconductor.org/packages/diffHic.

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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software
Version	1.45.0
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 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
System Requirements	C++, GNU make
URL

Suggests	BSgenome.Ecoli.NCBI.20080805, Matrix, testthat
Linking To	Rhtslib (>= 1.13.1), Rcpp
Enhances
Depends On Me
Imports Me	hicream
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	diffHic_1.45.0.tar.gz
Windows Binary (x86_64)	diffHic_1.45.0.zip
macOS Binary (big-sur-x86_64)	diffHic_1.45.0.tgz
macOS Binary (sonoma-arm64)	diffHic_1.45.0.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