diffHic
This is the development version of diffHic; for the stable release version, see diffHic.
All Bioconductor versions of diffHic
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: 3.24 · Package version: 1.45.0
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.
Details
| Version | 1.45.0 |
| License | GPL-3 |
| System Requirements | C++, GNU make |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11 years) |
| Downloads rank | 444 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/diffHic/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("diffHic")| diffHic Vignette | |
| Reference Manual | |
| NEWS | Text |
Download
Follow the 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 (arm64) | diffHic_1.45.0.tgz |
| macOS binary (x86_64) | 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 Downloads Report | Download Stats |
Dependencies
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), Rcpp
Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat
Reverse dependencies
Imports Me (1): hicream