recipe gothresher

GOThresher: a program to remove annotation biases from protein function annotation datasets

Homepage:

https://github.com/FriedbergLab/GOThresher

License:

GPL3 / GPL-3.0-only

Recipe:

/gothresher/meta.yaml

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

(downloads) docker_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 biopython:

depends matplotlib-base:

depends networkx:

depends numpy:

depends python:

depends xlsxwriter:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install gothresher

and update with::

   mamba update gothresher

To create a new environment, run:

mamba create --name myenvname gothresher

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/gothresher:<tag>

(see `gothresher/tags`_ for valid values for ``<tag>``)

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Link to this page

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