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SpectralTAD

SpectralTAD: Hierarchical TAD detection using spectral clustering


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SpectralTAD")

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("SpectralTAD")
SpectralTAD HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, FeatureExtraction, HiC, Sequencing, Software
Version 1.18.0
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
System Requirements
URL https://github.com/dozmorovlab/SpectralTAD
Bug Reports https://github.com/dozmorovlab/SpectralTAD/issues
See More
Suggests BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr
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Package Archives

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

Source Package SpectralTAD_1.18.0.tar.gz
Windows Binary SpectralTAD_1.18.0.zip
macOS Binary (x86_64) SpectralTAD_1.18.0.tgz
macOS Binary (arm64) SpectralTAD_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SpectralTAD
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpectralTAD
Bioc Package Browser https://code.bioconductor.org/browse/SpectralTAD/
Package Short Url https://bioconductor.org/packages/SpectralTAD/
Package Downloads Report Download Stats