:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-epialleler' .. highlight: bash bioconductor-epialleler ======================= .. conda:recipe:: bioconductor-epialleler :replaces_section_title: :noindex: Fast\, Epiallele\-Aware Methylation Caller and Reporter :homepage: https://bioconductor.org/packages/3.18/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 and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next\-generation sequencing data using binary alignment map \(BAM\) files as an input. Among other things\, this package can also extract methylation patterns and assess allele specificity of methylation. .. conda:package:: bioconductor-epialleler |downloads_bioconductor-epialleler| |docker_bioconductor-epialleler| :versions: ``1.10.0-0``,  ``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: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-variantannotation: ``>=1.48.0,<1.49.0`` :depends bioconductor-variantannotation: ``>=1.48.1,<1.49.0a0`` :depends bioconductor-zlibbioc: ``>=1.48.0,<1.49.0`` :depends bioconductor-zlibbioc: ``>=1.48.0,<1.49.0a0`` :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: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-epialleler/tags`_ for valid values for ````) .. |downloads_bioconductor-epialleler| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-epialleler.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-epialleler :alt: (downloads) .. |docker_bioconductor-epialleler| image:: https://quay.io/repository/biocontainers/bioconductor-epialleler/status :target: https://quay.io/repository/biocontainers/bioconductor-epialleler .. _`bioconductor-epialleler/tags`: https://quay.io/repository/biocontainers/bioconductor-epialleler?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html 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-epialleler/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-epialleler/README.html