Package: SpectralTAD
Title: SpectralTAD: Hierarchical TAD detection using spectral
        clustering
Version: 1.26.0
Authors@R: c(
    person(given = "Mikhail",
           family = "Dozmorov",
           role = c("aut", "cre"),
           email = "mikhail.dozmorov@gmail.com",
           comment = c(ORCID = "0000-0002-0086-8358")),
    person(given = "Kellen",
           family = "Cresswell",
           role = c("aut")),
    person(given = "John",
           family = "Stansfield",
           role = c("aut"))
           )
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.2.3
Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
        magrittr, HiCcompare, GenomicRanges, utils
Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
        microbenchmark, testthat, covr
Depends: R (>= 3.6)
VignetteBuilder: knitr
biocViews: Software, HiC, Sequencing, FeatureExtraction, Clustering
BugReports: https://github.com/dozmorovlab/SpectralTAD/issues
URL: https://github.com/dozmorovlab/SpectralTAD
Config/pak/sysreqs: make libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:50:13 UTC
RemoteUrl: https://github.com/bioc/SpectralTAD
RemoteRef: RELEASE_3_22
RemoteSha: 1a597b5116bffdc204a33487736f0f6845afae92
NeedsCompilation: no
Packaged: 2026-01-28 08:45:58 UTC; root
Author: Mikhail Dozmorov [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0086-8358>),
  Kellen Cresswell [aut],
  John Stansfield [aut]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Built: R 4.5.2; ; 2026-01-28 08:47:42 UTC; windows
