SpectralTAD

DOI: 10.18129/B9.bioc.SpectralTAD    

SpectralTAD: Hierarchical TAD detection using spectral clustering

Bioconductor version: Release (3.10)

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>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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 1.2.0
In Bioconductor since BioC 3.9 (R-3.6) (0.5 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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SpectralTAD_1.2.0.tar.gz
Windows Binary SpectralTAD_1.2.0.zip
Mac OS X 10.11 (El Capitan) SpectralTAD_1.2.0.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/
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