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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "sarks" in publications use:'
type: software
license: BSD-3-Clause
title: 'sarks: Suffix Array Kernel Smoothing for discovery of correlative sequence
  motifs and multi-motif domains'
version: 1.17.0
doi: 10.1093/bioinformatics/btz198
abstract: 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.
authors:
- family-names: Wylie
  given-names: Dennis
  email: denniscwylie@gmail.com
  orcid: https://orcid.org/0000-0003-0380-3549
preferred-citation:
  type: article
  title: 'SArKS: de novo discovery of gene expression regulatory motif sites and domains
    by suffix array kernel smoothing'
  authors:
  - family-names: Wylie
    given-names: Dennis C.
  - family-names: Hofmann
    given-names: Hans A.
  - family-names: Zemelman
    given-names: Boris V.
  year: '2019'
  journal: Bioinformatics
  doi: 10.1093/bioinformatics/btz198
  volume: '35'
  issue: '20'
  start: 3944-3952
repository: https://bioc.r-universe.dev
repository-code: https://github.com/denniscwylie/sarks
url: https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797
contact:
- family-names: Wylie
  given-names: Dennis
  email: denniscwylie@gmail.com
  orcid: https://orcid.org/0000-0003-0380-3549