recipe bioconductor-sarks

Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Homepage

https://bioconductor.org/packages/3.13/bioc/html/sarks.html

License

BSD_3_clause + file LICENSE

Recipe

/bioconductor-sarks/meta.yaml

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.

package bioconductor-sarks

(downloads) docker_bioconductor-sarks

Versions

1.4.0-01.2.0-11.2.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-sarks

and update with:

conda update bioconductor-sarks

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-sarks:<tag>

(see bioconductor-sarks/tags for valid values for <tag>)

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