recipe bioconductor-motifcounter

‘motifcounter’ provides motif matching, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higher-order background models and accounting for self-overlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide (or higher-order nucleotide) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for self-overlapping motif structures as exemplified by repeat-like or palindromic motifs, and allow to determine the p-value and fold-enrichment for a set of observed motif matches.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/motifcounter.html

License

GPL-2

Recipe

/bioconductor-motifcounter/meta.yaml

package bioconductor-motifcounter

(downloads) docker_bioconductor-motifcounter

Versions

1.8.0-1, 1.6.0-0, 1.4.0-0, 1.2.1-0

Depends
Required By

Installation

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

conda install bioconductor-motifcounter

and update with:

conda update bioconductor-motifcounter

or use the docker container:

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

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