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 (3.24)
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]
, Kellen Cresswell [aut], John Stansfield [aut]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>
citation("SpectralTAD")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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_1.29.2.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpectralTAD/ |
| Package Short Url | https://bioconductor.org/packages/SpectralTAD/ |
| Package Downloads Report | Download Stats |