multiHiCcompare

DOI: 10.18129/B9.bioc.multiHiCcompare    

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

Bioconductor version: Release (3.8)

multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.

Author: John Stansfield [aut, cre], Mikhail Dozmorov [aut]

Maintainer: John Stansfield <stansfieldjc at vcu.edu>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("multiHiCcompare", version = "3.8")

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("multiHiCcompare")

 

HTML R Script multiHiCcompare Vignette
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews HiC, Normalization, Sequencing, Software
Version 1.0.0
License MIT + file LICENSE
Depends R (>= 3.5.0)
Imports data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, metap, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb
LinkingTo
Suggests knitr, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me HiCcompare
Links To Me
Build Report  

Package Archives

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

Source Package multiHiCcompare_1.0.0.tar.gz
Windows Binary multiHiCcompare_1.0.0.zip
Mac OS X 10.11 (El Capitan) multiHiCcompare_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/multiHiCcompare
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/multiHiCcompare
Package Short Url http://bioconductor.org/packages/multiHiCcompare/
Package Downloads Report Download Stats

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