TADCompare

DOI: 10.18129/B9.bioc.TADCompare    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see TADCompare.

TADCompare: Identification and characterization of differential TADs

Bioconductor version: 3.13

TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.

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

Maintainer: Kellen Cresswell <cresswellkg at vcu.edu>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("TADCompare")

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("TADCompare")

 

HTML	R Script	Gene Ontology Enrichment Analysis
HTML	R Script	Input data formats
HTML	R Script	TAD comparison between two conditions
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, FeatureExtraction, HiC, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.0)
Imports	dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD
SystemRequirements
Enhances
URL	https://github.com/dozmorovlab/TADCompare
BugReports	https://github.com/dozmorovlab/TADCompare/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TADCompare_1.2.0.tar.gz
Windows Binary	TADCompare_1.2.0.zip
macOS 10.13 (High Sierra)	TADCompare_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TADCompare
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TADCompare
Package Short Url	https://bioconductor.org/packages/TADCompare/
Package Downloads Report	Download Stats