BIOCONDUCTOR . ORG {
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Title:
Bioconductor - sarks
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.
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Keywords {🔍}
bioconductor, package, sarks, packages, version, suffix, array, smoothing, release, source, kernel, sequence, motifs, domains, sequences, wylie, enter, install, license, reports, binary, learn, developers, started, software, discovery, multimotif, httpsacademicoupcombioinformaticsarticleabstract, expression, gene, based, dennis, installation, start, documentation, system, pdf, text, details, bioc, stats, url, macos, sarkstgz, repository, git, clone, code, registration, open,
Topics {✒️}
org/packages/sarks source repository /denniscwylie/sarks bug reports joint galaxy/bioconductor conference bioconductor release tgz source repository source package /bioinformatics/article-abstract/35/20/3944/5418797 https release differential expression statistics suffix array based //code bioconductor support site /bioinformatics/article-abstract/35/20/3944/5418797 /denniscwylie/sarks/issues false positive rates script reference manual package installed dennis wylie [aut gz windows binary git clone https correlative sequence motifs identifies sequence motifs tgz macos binary de novo discovery details biocviews binom system requirements package packages started install gene promoters macos binary sarks smooths sarks-vignette bioconductor //bioconductor sequence similarity input sequences discovered motifs wylie dc extended based 1093/bioinformatics/btz198 org registration open presence correlates numeric scores full set spatial proximity permutation testing cre] orcid hofmann ha
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