recipe bioconductor-epialleler

Fast, Epiallele-Aware Methylation Reporter

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/epialleleR.html

License:

Artistic-2.0

Recipe:

/bioconductor-epialleler/meta.yaml

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls hypermethylated epiallele frequencies at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Other functionality includes extracting methylation patterns, computing the empirical cumulative distribution function for per-read beta values, and testing the significance of the association between epiallele methylation status and base frequencies at particular genomic positions (SNPs).

package bioconductor-epialleler

versions:

1.8.1-0,  1.8.0-0,  1.6.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-rhtslib:

>=2.2.0,<2.3.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends bioconductor-zlibbioc:

>=1.46.0,<1.47.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

depends r-data.table:

depends r-rcpp:

depends r-stringi:

requirements:

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-epialleler

and update with::

   mamba update bioconductor-epialleler

To create a new environment, run:

mamba create --name myenvname bioconductor-epialleler

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-epialleler:<tag>

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

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