DOI: 10.18129/B9.bioc.SpectralTAD  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SpectralTAD.

SpectralTAD: Hierarchical TAD detection using spectral clustering

Bioconductor version: 3.16

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 gmail.com>

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


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biocViews Clustering, FeatureExtraction, HiC, Sequencing, Software
Version 1.14.1
In Bioconductor since BioC 3.9 (R-3.6) (4 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils
Suggests BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr
URL https://github.com/dozmorovlab/SpectralTAD
BugReports https://github.com/dozmorovlab/SpectralTAD/issues
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Source Package SpectralTAD_1.14.1.tar.gz
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