TADCompare

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TADCompare.

TADCompare: Identification and characterization of differential TADs


Bioconductor version: 3.12

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 "4.0") 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

Details

biocViews Clustering, FeatureExtraction, HiC, Sequencing, Software
Version 1.0.0
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
Bug Reports https://github.com/dozmorovlab/TADCompare/issues
See More
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_1.0.0.tar.gz
Windows Binary TADCompare_1.0.0.zip
macOS 10.13 (High Sierra) TADCompare_1.0.0.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 3.12 Source Archive