recipe bioconductor-alphamissenser

Accessing AlphaMissense Data Resources in R

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/AlphaMissenseR.html

License:

Artistic-2.0

Recipe:

/bioconductor-alphamissenser/meta.yaml

The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.

package bioconductor-alphamissenser

versions:

1.2.0-0

depends bioconductor-biocbaseutils:

>=1.8.0,<1.9.0

depends bioconductor-biocfilecache:

>=2.14.0,<2.15.0

depends r-base:

>=4.4,<4.5.0a0

depends r-curl:

depends r-dbi:

depends r-dplyr:

depends r-duckdb:

>=0.9.1

depends r-ggplot2:

depends r-memoise:

depends r-rjsoncons:

>=1.0.1

depends r-rlang:

depends r-spdl:

depends r-whisker:

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-alphamissenser

and update with::

   mamba update bioconductor-alphamissenser

To create a new environment, run:

mamba create --name myenvname bioconductor-alphamissenser

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-alphamissenser:<tag>

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

Download stats

Link to this page

Render an 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-alphamissenser/README.html)