recipe bioconductor-probamr

Generating SAM file for PSMs in shotgun proteomics data

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-probamr/meta.yaml

Links:

biotools: probamr, doi: 10.1074/mcp.M115.052860

Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

package bioconductor-probamr

(downloads) docker_bioconductor-probamr

versions:
1.34.0-01.32.0-01.28.0-01.26.0-01.24.0-11.24.0-01.22.0-01.20.0-01.18.0-1

1.34.0-01.32.0-01.28.0-01.26.0-01.24.0-11.24.0-01.22.0-01.20.0-01.18.0-11.16.0-01.14.0-01.12.0-01.10.0-01.8.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

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-rtracklayer:

>=1.60.0,<1.61.0

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-probamr

and update with::

   mamba update bioconductor-probamr

To create a new environment, run:

mamba create --name myenvname bioconductor-probamr

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-probamr:<tag>

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

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