- recipe proteomiqon-alignmentbasedquantstatistics
The tool ProteomIQon.AlignmentBasedQuantStatistics scores peptide ion quantifications obtained through alignment between runs.
- Homepage:
- Documentation:
https://csbiology.github.io/ProteomIQon/tools/AlignmentBasedQuantStatistics.html
- Developer docs:
- License:
MIT
- Recipe:
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¶
- Versions:
0.0.3-0,0.0.1-0- 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-alignmentbasedquantstatistics
to add into an existing workspace instead, run:
pixi add proteomiqon-alignmentbasedquantstatistics
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-alignmentbasedquantstatistics
Alternatively, to install into a new environment, run:
conda create -n envname proteomiqon-alignmentbasedquantstatistics
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-alignmentbasedquantstatistics:<tag>
(see proteomiqon-alignmentbasedquantstatistics/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-alignmentbasedquantstatistics/README.html)
