SpectralTAD
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SpectralTAD.
SpectralTAD: Hierarchical TAD detection using spectral clustering
Bioconductor version: 3.12
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("SpectralTAD")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| SpectralTAD | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, FeatureExtraction, HiC, Sequencing, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6) |
| Imports | dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges |
| System Requirements | |
| URL | https://github.com/dozmorovlab/SpectralTAD |
| Bug Reports | https://github.com/dozmorovlab/SpectralTAD/issues |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpectralTAD_1.6.0.tar.gz |
| Windows Binary | SpectralTAD_1.6.0.zip |
| macOS 10.13 (High Sierra) | SpectralTAD_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpectralTAD |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpectralTAD |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpectralTAD/ |
| Package Short Url | https://bioconductor.org/packages/SpectralTAD/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |