- 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:
- Documentation:
https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html
- Developer docs:
- License:
MIT
- Recipe:
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:
on dotnet-runtime
5.0.*on openssl
1.1.*
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install proteomiqon-proteininference
to add into an existing workspace instead, run:
pixi add proteomiqon-proteininference
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install proteomiqon-proteininference
Alternatively, to install into a new environment, run:
conda create -n envname proteomiqon-proteininference
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/proteomiqon-proteininference:<tag>
(see proteomiqon-proteininference/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/proteomiqon-proteininference/README.html)
