DESCRIPTION

Package: SpectralTAD
Title: SpectralTAD: Hierarchical TAD detection using spectral clustering
Version: 1.7.1
Author:
    Kellen Cresswell <cresswellkg@vcu.edu>,
    John Stansfield <stansfieldjc@vcu.edu>, 
    Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>
Maintainer: Kellen Cresswell <cresswellkg@vcu.edu>
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: 7.1.1
Imports: 
    dplyr,
    PRIMME,
    cluster,
    Matrix,
    parallel,
    BiocParallel,
    magrittr,
    HiCcompare,
    GenomicRanges
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