dozmorovlab/SpectralTAD: SpectralTAD: Hierarchical TAD detection using spectral clustering

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.

Getting started

Package details

Author Kellen Cresswell <cresswellkg@vcu.edu>, John Stansfield <stansfieldjc@vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>
Bioconductor views Clustering FeatureExtraction HiC Sequencing Software
MaintainerKellen Cresswell <cresswellkg@vcu.edu>
LicenseMIT + file LICENSE
Version1.2.1
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("dozmorovlab/SpectralTAD")
dozmorovlab/SpectralTAD documentation built on March 17, 2020, 3:39 a.m.