recipe bioconductor-rgadem

de novo motif discovery

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-rgadem/meta.yaml

Links:

biotools: rgadem, doi: 10.1371/journal.pone.0016432

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.

package bioconductor-rgadem

versions:

2.50.0-0,  2.48.0-0,  2.46.0-1,  2.46.0-0,  2.42.0-2,  2.42.0-1,  2.42.0-0,  2.40.0-0,  2.38.0-1, 

2.50.0-0,  2.48.0-0,  2.46.0-1,  2.46.0-0,  2.42.0-2,  2.42.0-1,  2.42.0-0,  2.40.0-0,  2.38.0-1,  2.38.0-0,  2.36.0-0,  2.34.0-0,  2.32.0-1,  2.30.0-0,  2.28.0-0,  2.26.0-0,  2.24.0-0,  2.22.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-bsgenome:

>=1.70.1,<1.71.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-seqlogo:

>=1.68.0,<1.69.0

depends bioconductor-seqlogo:

>=1.68.0,<1.69.0a0

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-rgadem

and update with::

   mamba update bioconductor-rgadem

To create a new environment, run:

mamba create --name myenvname bioconductor-rgadem

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-rgadem:<tag>

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

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