:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-methylkit' .. highlight: bash bioconductor-methylkit ====================== .. conda:recipe:: bioconductor-methylkit :replaces_section_title: :noindex: DNA methylation analysis from high\-throughput bisulfite sequencing results :homepage: https://bioconductor.org/packages/3.18/bioc/html/methylKit.html :license: Artistic-2.0 :recipe: /`bioconductor-methylkit `_/`meta.yaml `_ :links: biotools: :biotools:`methylkit` methylKit is an R package for DNA methylation analysis and annotation from high\-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants\, but also target\-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base\-pair resolution 5hmC data from experimental protocols such as oxBS\-Seq and TAB\-Seq. Methylation calling can be performed directly from Bismark aligned BAM files. .. conda:package:: bioconductor-methylkit |downloads_bioconductor-methylkit| |docker_bioconductor-methylkit| :versions: .. raw:: html
1.28.0-01.26.0-01.24.0-11.24.0-01.20.0-21.20.0-11.20.0-01.18.0-01.16.1-0 ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-1``,  ``1.24.0-0``,  ``1.20.0-2``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.1-0``,  ``1.16.0-0``,  ``1.14.1-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.8.1-0``,  ``1.8.0-0``,  ``1.6.3-0``,  ``1.4.0-0``,  ``1.2.4-0``,  ``1.0.0-0``,  ``0.99.2-0`` .. raw:: html
:depends bioconductor-fastseg: ``>=1.48.0,<1.49.0`` :depends bioconductor-fastseg: ``>=1.48.0,<1.49.0a0`` :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-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-limma: ``>=3.58.1,<3.59.0a0`` :depends bioconductor-qvalue: ``>=2.34.0,<2.35.0`` :depends bioconductor-qvalue: ``>=2.34.0,<2.35.0a0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0a0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0`` :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-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-data.table: ``>=1.9.6`` :depends r-emdbook: :depends r-gtools: :depends r-kernsmooth: :depends r-mclust: :depends r-mgcv: :depends r-r.utils: :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-methylkit and update with:: mamba update bioconductor-methylkit To create a new environment, run:: mamba create --name myenvname bioconductor-methylkit 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-methylkit: (see `bioconductor-methylkit/tags`_ for valid values for ````) .. |downloads_bioconductor-methylkit| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-methylkit.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-methylkit :alt: (downloads) .. |docker_bioconductor-methylkit| image:: https://quay.io/repository/biocontainers/bioconductor-methylkit/status :target: https://quay.io/repository/biocontainers/bioconductor-methylkit .. _`bioconductor-methylkit/tags`: https://quay.io/repository/biocontainers/bioconductor-methylkit?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-methylkit/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-methylkit/README.html