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HiCcompare

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

Bioconductor version: Release (3.17)

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: Mikhail Dozmorov [aut, cre] , Kellen Cresswell [aut], John Stansfield [aut]

Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>

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

Installation

To install this package, start R (version "4.3") 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 1.22.1
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), dplyr
Imports data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
Linking To
Suggests knitr, rmarkdown, testthat, multiHiCcompare
System Requirements
Enhances
URL https://github.com/dozmorovlab/HiCcompare
Bug Reports https://github.com/dozmorovlab/HiCcompare/issues
See More
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_1.22.1.tar.gz
Windows Binary HiCcompare_1.22.1.zip
macOS Binary (x86_64) HiCcompare_1.22.1.tgz
macOS Binary (arm64) HiCcompare_1.22.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCcompare
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCcompare
Bioc Package Browser https://code.bioconductor.org/browse/HiCcompare/
Package Short Url https://bioconductor.org/packages/HiCcompare/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive