Package: sarks
Title: Suffix Array Kernel Smoothing for discovery of correlative
        sequence motifs and multi-motif domains
Version: 1.25.0
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
Config/pak/sysreqs: make default-jdk zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:52:02 UTC
RemoteUrl: https://github.com/bioc/sarks
RemoteRef: HEAD
RemoteSha: 14425d46040248f81ae07b9c8bf8f61286cb18ac
NeedsCompilation: no
Packaged: 2026-07-03 18:36:17 UTC; root
Author: Dennis Wylie [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0380-3549>)
Maintainer: Dennis Wylie <denniscwylie@gmail.com>