recipe bioconductor-alphabeta

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/AlphaBeta.html

License:

GPL-3

Recipe:

/bioconductor-alphabeta/meta.yaml

AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze 'germline' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze 'somatic' epimutations in the context of plant development and aging.

package bioconductor-alphabeta

versions:

1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0, 

1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

>=1.10

depends r-dplyr:

>=0.7

depends r-expm:

>=0.999-4

depends r-ggplot2:

>=3.2

depends r-gtools:

>=3.8.0

depends r-igraph:

>=1.2.4

depends r-optimx:

>=2018-7.10

depends r-plotly:

>=4.9

depends r-stringr:

>=1.3

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-alphabeta

and update with::

   mamba update bioconductor-alphabeta

To create a new environment, run:

mamba create --name myenvname bioconductor-alphabeta

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-alphabeta:<tag>

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

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Link to this page

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