To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HiCcompare")

In most cases, you don't need to download the package archive at all.

HiCcompare

DOI: 10.18129/B9.bioc.HiCcompare    

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

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

Bioconductor version: Development (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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HiCcompare")

Documentation

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

Details

biocViews HiC, Normalization, Sequencing, Software
Version 1.1.0
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
LinkingTo
Suggests knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package HiCcompare_1.1.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) HiCcompare_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCcompare
Package Short Url http://bioconductor.org/packages/HiCcompare/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: