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>

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

Installation

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


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, FeatureExtraction, HiC, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0)
Imports	dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot
System Requirements
URL	https://github.com/dozmorovlab/TADCompare
Bug Reports	https://github.com/dozmorovlab/TADCompare/issues

Suggests	BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	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
Bioc Package Browser	https://code.bioconductor.org/browse/TADCompare/
Package Short Url	https://bioconductor.org/packages/TADCompare/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive