recipe proteomiqon-proteininference

MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.

Homepage:

https://csbiology.github.io/ProteomIQon/

Documentation:

https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html

Developer docs:

https://github.com/CSBiology/ProteomIQon

License:

MIT

Recipe:

/proteomiqon-proteininference/meta.yaml

MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. This process is not as straightforward as one might think at a first glance on the subject, since the peptide-to-protein mapping is not necessarily a one-to-one relationship but in many cases a one-to-many relationship. This is due to the fact that many proteins share peptides with an identical sequence, e.g. two proteins originating from two different splice variants of the same gene. The ProteinInference tool relies on the concepts of protein groups and peptide evidence classes.

package proteomiqon-proteininference

versions:

0.0.7-1,  0.0.7-0,  0.0.6-0,  0.0.5-0,  0.0.4-0

depends dotnet-runtime:

5.0.*

depends openssl:

1.1.*

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 proteomiqon-proteininference

and update with::

   mamba update proteomiqon-proteininference

To create a new environment, run:

mamba create --name myenvname proteomiqon-proteininference

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/proteomiqon-proteininference:<tag>

(see `proteomiqon-proteininference/tags`_ for valid values for ``<tag>``)

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