SpectralTAD

DOI: 10.18129/B9.bioc.SpectralTAD    

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

SpectralTAD: Hierarchical TAD detection using spectral clustering

Bioconductor version: Development (3.15)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpectralTAD")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Clustering, FeatureExtraction, HiC, Sequencing, Software
Version 1.11.0
In Bioconductor since BioC 3.9 (R-3.6) (2.5 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
Windows Binary
macOS 10.13 (High Sierra)
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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