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

SpectralTAD: Hierarchical TAD detection using spectral clustering

Bioconductor version: Development (3.20)

SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.

Author: Mikhail Dozmorov [aut, cre] , Kellen Cresswell [aut], John Stansfield [aut]

Maintainer: Mikhail Dozmorov <mikhail.dozmorov at>

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


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

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

# The following initializes usage of Bioc devel


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:

SpectralTAD HTML R Script
Reference Manual PDF


biocViews Clustering, FeatureExtraction, HiC, Sequencing, Software
Version 1.21.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils
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Suggests BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr
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Follow Installation instructions to use this package in your R session.

Source Package SpectralTAD_1.21.0.tar.gz
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macOS Binary (x86_64) SpectralTAD_1.21.0.tgz
macOS Binary (arm64) SpectralTAD_1.21.0.tgz
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