Package: sarks
Title: Suffix Array Kernel Smoothing for discovery of correlative
        sequence motifs and multi-motif domains
Version: 1.23.0
Authors@R: 
    person(given = "Dennis",
           family = "Wylie",
           role = c("aut", "cre"),
           email = "denniscwylie@gmail.com",
           comment = c(ORCID = "0000-0003-0380-3549"))
Description: Suffix Array Kernel Smoothing (see
    https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797),
    or SArKS, identifies sequence motifs whose presence correlates
    with numeric scores (such as differential expression statistics)
    assigned to the sequences (such as gene promoters). SArKS smooths
    over sequence similarity, quantified by location within a suffix
    array based on the full set of input sequences. A second round of
    smoothing over spatial proximity within sequences reveals multi-motif
    domains. Discovered motifs can then be merged or extended based on
    adjacency within MMDs. False positive rates are estimated and controlled
    by permutation testing.
Depends: R (>= 4.0)
Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom
Suggests: RUnit, BiocGenerics, ggplot2
biocViews: MotifDiscovery, GeneRegulation, GeneExpression,
        Transcriptomics, RNASeq, DifferentialExpression,
        FeatureExtraction
SystemRequirements: Java (>= 1.8)
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 6.1.1
BugReports: https://github.com/denniscwylie/sarks/issues
URL:
        https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797,
        https://github.com/denniscwylie/sarks
git_url: https://git.bioconductor.org/packages/sarks
git_branch: devel
git_last_commit: 5f25697
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-10-31
NeedsCompilation: no
Packaged: 2025-10-31 23:56:12 UTC; biocbuild
Author: Dennis Wylie [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0380-3549>)
Maintainer: Dennis Wylie <denniscwylie@gmail.com>
