recipe bioconductor-motiftestr

Perform key tests for binding motifs in sequence data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/motifTestR.html

License:

GPL-3

Recipe:

/bioconductor-motiftestr/meta.yaml

Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.

package bioconductor-motiftestr

versions:

1.2.1-0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-universalmotif:

>=1.24.0,<1.25.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

>=3.5.0

depends r-harmonicmeanp:

depends r-matrixstats:

depends r-patchwork:

depends r-rlang:

requirements:

additional platforms:

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-motiftestr

and update with::

   mamba update bioconductor-motiftestr

To create a new environment, run:

mamba create --name myenvname bioconductor-motiftestr

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-motiftestr:<tag>

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

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