diffHic

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see diffHic.

Differential Analyis of Hi-C Data

Bioconductor version: 3.18

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>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")

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 1.34.0

In Bioconductor since BioC 3.1 (R-3.2) (9 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++11, GNU make

URL

Suggests BSgenome.Ecoli.NCBI.20080805, Matrix, testthat

Linking To Rhtslib(>= 1.13.1), zlibbioc, Rcpp

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package diffHic_1.34.0.tar.gz

Windows Binary diffHic_1.34.0.zip (64-bit only)

macOS Binary (x86_64) diffHic_1.34.0.tgz

macOS Binary (arm64) diffHic_1.34.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/diffHic

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/diffHic

Bioc Package Browser https://code.bioconductor.org/browse/diffHic/

Package Short Url https://bioconductor.org/packages/diffHic/

Package Downloads Report Download Stats