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TADCompare: Identification and characterization of differential TADs

Bioconductor version: Release (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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Gene Ontology Enrichment Analysis HTML R Script
Input data formats HTML R Script
TAD comparison between two conditions HTML R Script
Reference Manual PDF


biocViews Clustering, FeatureExtraction, HiC, Sequencing, Software
Version 1.14.0
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
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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_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) TADCompare_1.14.0.tgz
macOS Binary (arm64) TADCompare_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive