:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-epimutacions' .. highlight: bash bioconductor-epimutacions ========================= .. conda:recipe:: bioconductor-epimutacions :replaces_section_title: :noindex: Robust outlier identification for DNA methylation data :homepage: https://bioconductor.org/packages/3.18/bioc/html/epimutacions.html :license: MIT + file LICENSE :recipe: /`bioconductor-epimutacions `_/`meta.yaml `_ The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA\, Multivariate linear models\, isolation forest\, robust mahalanobis distance\, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel \(composed of healthy individuals\) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations. .. conda:package:: bioconductor-epimutacions |downloads_bioconductor-epimutacions| |docker_bioconductor-epimutacions| :versions: ``1.6.1-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.2.0-0`` :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-annotationdbi: ``>=1.64.1,<1.65.0a0`` :depends bioconductor-annotationhub: ``>=3.10.0,<3.11.0`` :depends bioconductor-annotationhub: ``>=3.10.0,<3.11.0a0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-biomart: ``>=2.58.0,<2.59.0`` :depends bioconductor-biomart: ``>=2.58.0,<2.59.0a0`` :depends bioconductor-bumphunter: ``>=1.44.0,<1.45.0`` :depends bioconductor-bumphunter: ``>=1.44.0,<1.45.0a0`` :depends bioconductor-ensembldb: ``>=2.26.0,<2.27.0`` :depends bioconductor-ensembldb: ``>=2.26.0,<2.27.0a0`` :depends bioconductor-epimutacionsdata: ``>=1.6.0,<1.7.0`` :depends bioconductor-epimutacionsdata: ``>=1.6.0,<1.7.0a0`` :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0`` :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0a0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicfeatures: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-gviz: ``>=1.46.0,<1.47.0`` :depends bioconductor-gviz: ``>=1.46.1,<1.47.0a0`` :depends bioconductor-homo.sapiens: ``>=1.3.0,<1.4.0`` :depends bioconductor-homo.sapiens: ``>=1.3.1,<1.4.0a0`` :depends bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19: ``>=0.6.0,<0.7.0`` :depends bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19: ``>=0.6.1,<0.7.0a0`` :depends bioconductor-illuminahumanmethylation450kmanifest: ``>=0.4.0,<0.5.0`` :depends bioconductor-illuminahumanmethylation450kmanifest: ``>=0.4.0,<0.5.0a0`` :depends bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19: ``>=0.6.0,<0.7.0`` :depends bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19: ``>=0.6.0,<0.7.0a0`` :depends bioconductor-illuminahumanmethylationepicmanifest: ``>=0.3.0,<0.4.0`` :depends bioconductor-illuminahumanmethylationepicmanifest: ``>=0.3.0,<0.4.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-minfi: ``>=1.48.0,<1.49.0`` :depends bioconductor-minfi: ``>=1.48.0,<1.49.0a0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-txdb.hsapiens.ucsc.hg18.knowngene: ``>=3.2.0,<3.3.0`` :depends bioconductor-txdb.hsapiens.ucsc.hg18.knowngene: ``>=3.2.2,<3.3.0a0`` :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.0,<3.3.0`` :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.2,<3.3.0a0`` :depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene: ``>=3.18.0,<3.19.0`` :depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene: ``>=3.18.0,<3.19.0a0`` :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-ggplot2: :depends r-ggrepel: :depends r-gridextra: :depends r-isotree: :depends r-matrixstats: :depends r-purrr: :depends r-reshape2: :depends r-robustbase: :depends r-tibble: :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-epimutacions and update with:: mamba update bioconductor-epimutacions To create a new environment, run:: mamba create --name myenvname bioconductor-epimutacions 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-epimutacions: (see `bioconductor-epimutacions/tags`_ for valid values for ````) .. |downloads_bioconductor-epimutacions| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-epimutacions.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-epimutacions :alt: (downloads) .. |docker_bioconductor-epimutacions| image:: https://quay.io/repository/biocontainers/bioconductor-epimutacions/status :target: https://quay.io/repository/biocontainers/bioconductor-epimutacions .. _`bioconductor-epimutacions/tags`: https://quay.io/repository/biocontainers/bioconductor-epimutacions?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-epimutacions/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-epimutacions/README.html