DOI: 10.18129/B9.bioc.diffHic  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see diffHic.

Differential Analyis of Hi-C Data

Bioconductor version: 3.16

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")):


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


biocViews Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software
Version 1.30.0
In Bioconductor since BioC 3.1 (R-3.2) (8 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
LinkingTo Rhtslib(>= 1.13.1), zlibbioc, Rcpp
Suggests BSgenome.Ecoli.NCBI.20080805, Matrix, testthat
SystemRequirements C++11, GNU make
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package diffHic_1.30.0.tar.gz
Windows Binary diffHic_1.30.0.zip (64-bit only)
macOS Binary (x86_64) diffHic_1.30.0.tgz
macOS Binary (arm64) diffHic_1.30.0.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/
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