recipe bioconductor-damefinder

Finds DAMEs - Differential Allelicly MEthylated regions

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-damefinder/meta.yaml

'DAMEfinder' offers functionality for taking methtuple or bismark outputs to calculate ASM scores and compute DAMEs. It also offers nice visualization of methyl-circle plots.

package bioconductor-damefinder

versions:

1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.1-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-bumphunter:

>=1.48.0,<1.49.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-variantannotation:

>=1.52.0,<1.53.0

depends r-base:

>=4.4,<4.5.0a0

depends r-cowplot:

depends r-ggplot2:

depends r-plyr:

depends r-readr:

depends r-reshape2:

depends r-stringr:

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-damefinder

and update with::

   mamba update bioconductor-damefinder

To create a new environment, run:

mamba create --name myenvname bioconductor-damefinder

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-damefinder:<tag>

(see `bioconductor-damefinder/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-damefinder/README.html)