- recipe proteomiqon-labelfreeproteinquantification
The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.
- Homepage:
- Documentation:
https://csbiology.github.io/ProteomIQon/tools/LabelFreeProteinQuantification.html
- Developer docs:
- License:
MIT
- Recipe:
After quantification and protein inference are performed, it is known which peptide originated from which protein, as well as the intensity of each peptide. The information available for each peptide now needs to be aggragated for their proteins. This tool performs the aggregation from the peptides to the protein in several steps. The first two aggregation steps are optional. One of them is the aggregation based on charge state. Peptides with the same sequence and modifications, but different charge states are being aggregated. The next optional step does the same for peptides with the same sequence, but different modifications. Those steps build upon each other. The last step is the aggregation of all peptides of a protein. The result of each aggregation step is given as a tab separated file. The aggregation is performed according to the given parameters for each step. If an optional aggregation is not performed, the next step takes the result from the prior aggregation. For example, if aggregation by charge and modification are skipped, the protein aggregation is performed on previously unaggregated peptides, where a peptidesequence can occur with different charge states and modifications.
- package proteomiqon-labelfreeproteinquantification¶
- Versions:
0.0.3-1,0.0.1-1,0.0.1-0- 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-labelfreeproteinquantification
to add into an existing workspace instead, run:
pixi add proteomiqon-labelfreeproteinquantification
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-labelfreeproteinquantification
Alternatively, to install into a new environment, run:
conda create -n envname proteomiqon-labelfreeproteinquantification
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-labelfreeproteinquantification:<tag>
(see proteomiqon-labelfreeproteinquantification/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-labelfreeproteinquantification/README.html)
