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 (3.12)

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 method for detecting differences between Hi-C datasets.

Author: John Stansfield <stansfieldjc at vcu.edu>, Kellen Cresswell <cresswellkg at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Maintainer: John Stansfield <stansfieldjc at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

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

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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

Details

biocViews HiC, Normalization, Sequencing, Software
Version 1.11.1
In Bioconductor since BioC 3.6 (R-3.4) (3 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, rhdf5
LinkingTo
Suggests knitr, rmarkdown, testthat, multiHiCcompare
SystemRequirements
Enhances
URL https://github.com/dozmorovlab/HiCcompare
BugReports https://github.com/dozmorovlab/HiCcompare/issues
Depends On Me
Imports Me multiHiCcompare, SpectralTAD, TADCompare
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package HiCcompare_1.11.1.tar.gz
Windows Binary HiCcompare_1.11.1.zip
macOS 10.13 (High Sierra) HiCcompare_1.11.1.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/
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: