SpectralTAD

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

SpectralTAD: Hierarchical TAD detection using spectral clustering

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-0086-8358 , Kellen Cresswell [aut], John Stansfield [aut]

Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>

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

Mikhail Dozmorov, Kellen Cresswell, John Stansfield. SpectralTAD: SpectralTAD: Hierarchical TAD detection using spectral clustering. doi:10.18129/B9.bioc.SpectralTAD, R package version 1.29.2, https://bioconductor.org/packages/SpectralTAD.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, FeatureExtraction, HiC, Sequencing, Software
Version	1.29.2
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	dplyr, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils
System Requirements
URL	https://github.com/dozmorovlab/SpectralTAD
Bug Reports	https://github.com/dozmorovlab/SpectralTAD/issues

Suggests	BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	TADCompare
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SpectralTAD_1.29.2.tar.gz
Windows Binary (x86_64)	SpectralTAD_1.29.2.zip
macOS Binary (big-sur-x86_64)	SpectralTAD_1.29.2.tgz
macOS Binary (sonoma-arm64)	SpectralTAD_1.29.2.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