This is the development version of SpectralTAD; for the stable release version, see SpectralTAD.
SpectralTAD: Hierarchical TAD detection using spectral clusteringBioconductor version: Development (3.22)
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, entercitation("SpectralTAD")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpectralTAD")Follow Installation instructions to use this package in your R session.
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