SpectralTAD

DOI: 10.18129/B9.bioc.SpectralTAD    

SpectralTAD: Hierarchical TAD detection using spectral clustering

Bioconductor version: Release (3.15)

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: Kellen Cresswell <cresswellkg at vcu.edu>, John Stansfield <stansfieldjc at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Maintainer: Kellen Cresswell <cresswellkg at vcu.edu>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	SpectralTAD
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, FeatureExtraction, HiC, Sequencing, Software
Version	1.12.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges
LinkingTo
Suggests	BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr
SystemRequirements
Enhances
URL	https://github.com/dozmorovlab/SpectralTAD
BugReports	https://github.com/dozmorovlab/SpectralTAD/issues
Depends On Me
Imports Me
Suggests Me	TADCompare
Links To Me
Build Report

Package Archives

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

Source Package	SpectralTAD_1.12.0.tar.gz
Windows Binary	SpectralTAD_1.12.0.zip
macOS Binary (x86_64)	SpectralTAD_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpectralTAD
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpectralTAD
Package Short Url	https://bioconductor.org/packages/SpectralTAD/
Package Downloads Report	Download Stats