TADCompare

DOI: 10.18129/B9.bioc.TADCompare    

TADCompare: Identification and characterization of differential TADs

Bioconductor version: Release (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 (!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 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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
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_1.0.0.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
Package Short Url https://bioconductor.org/packages/TADCompare/
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: