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TADCompare

This is the development version of TADCompare; for the stable release version, see TADCompare.

TADCompare: Identification and characterization of differential TADs

Bioconductor version: Development (3.18)

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

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

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot
Linking To
Suggests BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD
System Requirements
Enhances
URL https://github.com/dozmorovlab/TADCompare
Bug Reports https://github.com/dozmorovlab/TADCompare/issues
See More
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_1.11.0.tar.gz
Windows Binary TADCompare_1.11.0.zip
macOS Binary (x86_64) TADCompare_1.11.0.tgz
macOS Binary (arm64) TADCompare_1.11.0.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