Package: SpectralTAD
Title: SpectralTAD: Hierarchical TAD detection using spectral
        clustering
Version: 1.25.0
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
git_url: https://git.bioconductor.org/packages/SpectralTAD
git_branch: devel
git_last_commit: 23faf2a
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 02:20:27 UTC; biocbuild
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 4.5.0; ; 2025-06-05 14:06:52 UTC; windows
