- recipe bioconductor-pgca
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
- Homepage:
- License:
GPL (>= 2)
- Recipe:
Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers.
- package bioconductor-pgca¶
- Versions:
1.34.0-0,1.30.0-0,1.26.0-0,1.24.0-0,1.22.0-0,1.18.0-0,1.16.0-0,1.14.0-1,1.14.0-0,1.34.0-0,1.30.0-0,1.26.0-0,1.24.0-0,1.22.0-0,1.18.0-0,1.16.0-0,1.14.0-1,1.14.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.8.0-0,1.6.1-0- Depends:
on r-base
>=4.5,<4.6.0a0
- 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 bioconductor-pgca
to add into an existing workspace instead, run:
pixi add bioconductor-pgca
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 bioconductor-pgca
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-pgca
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/bioconductor-pgca:<tag>
(see bioconductor-pgca/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/bioconductor-pgca/README.html)
