TADCompare

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see TADCompare.

TADCompare: Identification and characterization of differential TADs

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-0086-8358 , 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 "4.5") 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 1.18.0

In Bioconductor since BioC 3.12 (R-4.0) (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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Package Archives

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

Source Package TADCompare_1.18.0.tar.gz

Windows Binary (x86_64) TADCompare_1.18.0.zip (64-bit only)

macOS Binary (x86_64) TADCompare_1.18.0.tgz

macOS Binary (arm64) TADCompare_1.18.0.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/

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