recipe bioconductor-rfpred

Assign rfPred functional prediction scores to a missense variants list

Homepage:

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

License:

GPL (>=2 )

Recipe:

/bioconductor-rfpred/meta.yaml

Links:

biotools: rfpred, doi: 10.1101/037127

Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to download the TabixFile and index (approximately 3.3 Go).

package bioconductor-rfpred

versions:

1.44.0-1,  1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.32.0-2,  1.32.0-1,  1.32.0-0, 

1.44.0-1,  1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.32.0-2,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0a0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

requirements:

additional platforms:

linux-aarch64

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-rfpred

and update with::

   mamba update bioconductor-rfpred

To create a new environment, run:

mamba create --name myenvname bioconductor-rfpred

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-rfpred:<tag>

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

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