HiCcompare

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see HiCcompare.

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets


Bioconductor version: 3.7

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust permutation method for detecting differences between Hi-C datasets.

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

Maintainer: John Stansfield <stansfieldjc at vcu.edu>

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

Installation

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


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

BiocManager::install("HiCcompare")

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("HiCcompare")
HiCcompare Usage Vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews HiC, Normalization, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License MIT + file LICENSE
Depends R (>= 3.4.0), dplyr
Imports data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq, KernSmooth, methods, utils, graphics, pheatmap, gtools
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Suggests knitr, rmarkdown, testthat
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Package Archives

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

Source Package HiCcompare_1.2.0.tar.gz
Windows Binary HiCcompare_1.2.0.zip
Mac OS X 10.11 (El Capitan) HiCcompare_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCcompare
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCcompare
Package Short Url https://bioconductor.org/packages/HiCcompare/
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Old Source Packages for BioC 3.7 Source Archive