- recipe gothresher
GOThresher: a program to remove annotation biases from protein function annotation datasets
- Homepage:
- License:
GPL3 / GPL-3.0-only
- Recipe:
GOThresher removes annotation bias from GAF files based on GO term information content, GO evidence, annotation source, number of proteins annotated from a given source, and date. GOThresher accepts one or more GAF files as input. The motivation for GOThresher lies in the observation that protein function annotations are biased due to high throughput experimental studies. Removing such annotation biases can help present a more balanced picture of protein annotations for a given organism or set of proteins.
- package gothresher¶
- Versions:
1.0.29-0,1.0.28-0,1.0.27-0,1.0.26-0,1.0.24-0,1.0.21-0- Depends:
on biopython
on matplotlib-base
on networkx
on numpy
on python
on xlsxwriter
- 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 gothresher
to add into an existing workspace instead, run:
pixi add gothresher
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 gothresher
Alternatively, to install into a new environment, run:
conda create -n envname gothresher
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/gothresher:<tag>
(see gothresher/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/gothresher/README.html)
