recipe proteomiqon-alignmentbasedquantstatistics

The tool ProteomIQon.AlignmentBasedQuantStatistics scores peptide ion quantifications obtained through alignment between runs.

Homepage:

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

Documentation:

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

Developer docs:

https://github.com/CSBiology/ProteomIQon

License:

MIT

Recipe:

/proteomiqon-alignmentbasedquantstatistics/meta.yaml

MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. Due to the acquisition method for MS2, not every peptide ion present can be identified in every run. One approach to mitigate this problem is to align information obtained from similar runs to the current run, therefore getting more quantifications. This tool scores the quantifications obtained through alignment based on peak and run properties to obtain a measurement of reliability for the alignments.

package proteomiqon-alignmentbasedquantstatistics

(downloads) docker_proteomiqon-alignmentbasedquantstatistics

versions:

0.0.3-0,  0.0.1-0

depends dotnet-runtime:

5.0.*

depends openssl:

1.1.*

requirements:

additional platforms:

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-alignmentbasedquantstatistics

and update with::

   mamba update proteomiqon-alignmentbasedquantstatistics

To create a new environment, run:

mamba create --name myenvname proteomiqon-alignmentbasedquantstatistics

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-alignmentbasedquantstatistics:<tag>

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

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