recipe rbpbench

Evaluate CLIP-seq and other genomic region data using a comprehensive collection of known RBP binding motifs

Homepage:

https://github.com/michauhl/RBPBench

License:

MIT

Recipe:

/rbpbench/meta.yaml

package rbpbench

versions:

1.0.1-0,  1.0-0,  0.9-0,  0.8.1-0,  0.8-0,  0.7-0,  0.6-1,  0.6-0,  0.5-0, 

1.0.1-0,  1.0-0,  0.9-0,  0.8.1-0,  0.8-0,  0.7-0,  0.6-1,  0.6-0,  0.5-0,  0.4-0,  0.3-0,  0.2-0,  0.1-0

depends bedtools:

depends goatools:

depends infernal:

depends logomaker:

depends markdown:

depends matplotlib-venn:

depends meme:

>=5.0

depends packaging:

depends plotly:

depends python:

<3.12

depends scikit-learn:

depends scipy:

depends textdistance:

depends upsetplot:

>=0.9

depends venn:

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 rbpbench

and update with::

   mamba update rbpbench

To create a new environment, run:

mamba create --name myenvname rbpbench

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/rbpbench:<tag>

(see `rbpbench/tags`_ for valid values for ``<tag>``)

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