recipe bioconductor-proteodisco

Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/ProteoDisco.html

License:

GPL-3

Recipe:

/bioconductor-proteodisco/meta.yaml

ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

package bioconductor-proteodisco

versions:

1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-cleaver:

>=1.38.0,<1.39.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends bioconductor-xvector:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-checkmate:

>=2.0.0

depends r-dplyr:

>=1.0.6

depends r-parallellogger:

>=2.0.1

depends r-plyr:

>=1.8.6

depends r-rlang:

>=0.4.11

depends r-tibble:

>=3.1.2

depends r-tidyr:

>=1.1.3

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-proteodisco

and update with::

   mamba update bioconductor-proteodisco

To create a new environment, run:

mamba create --name myenvname bioconductor-proteodisco

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-proteodisco:<tag>

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

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Link to this page

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