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Bioconductor - diffHic (development version)

diffHic

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

Differential Analysis of Hi-C Data

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 Details biocViews Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software Version 1.41.0 In Bioconductor since BioC 3.1 (R-3.2) (10 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 See More Package Archives

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

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