recipe bioconductor-motifcounter

R package for analysing TFBSs in DNA sequences

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/motifcounter.html

License:

GPL-2

Recipe:

/bioconductor-motifcounter/meta.yaml

'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.

package bioconductor-motifcounter

versions:

1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.18.0-2,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-1, 

1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.18.0-2,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.6.0-0,  1.4.0-0,  1.2.1-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-motifcounter

and update with::

   mamba update bioconductor-motifcounter

To create a new environment, run:

mamba create --name myenvname bioconductor-motifcounter

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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