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 (3.19)

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 "4.4") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, FeatureExtraction, HiC, Sequencing, Software
Version	1.13.3
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, SpectralTAD, magick, qpdf
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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