recipe bioconductor-proteingymr

Programmatic access to ProteinGym datasets in R/Bioconductor

Homepage:

https://bioconductor.org/packages/3.20/data/experiment/html/ProteinGymR.html

License:

Artistic-2.0

Recipe:

/bioconductor-proteingymr/meta.yaml

The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. Deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. AlphaMissense pathogenicity scores for ~1.6 M substitutions in the ProteinGym DMS data, and 3. five performance metrics for 62 variant prediction models in a zero-shot setting.

package bioconductor-proteingymr

(downloads) docker_bioconductor-proteingymr

versions:

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 bioconductor-proteingymr

and update with::

   mamba update bioconductor-proteingymr

To create a new environment, run:

mamba create --name myenvname bioconductor-proteingymr

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/bioconductor-proteingymr:<tag>

(see `bioconductor-proteingymr/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-proteingymr/README.html)