:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-methodical' .. highlight: bash bioconductor-methodical ======================= .. conda:recipe:: bioconductor-methodical :replaces_section_title: :noindex: Discovering genomic regions where methylation is strongly associated with transcriptional activity :homepage: https://bioconductor.org/packages/3.22/bioc/html/methodical.html :license: GPL (>= 3) :recipe: /`bioconductor-methodical `_/`meta.yaml `_ DNA methylation is generally considered to be associated with transcriptional silencing. However\, comprehensive\, genome\-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition\, Methodical enables housing DNA methylation data from diverse sources \(e.g. WGBS\, RRBS and methylation arrays\) with a common framework\, lifting over DNA methylation data between different genome builds and creating base\-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites. .. conda:package:: bioconductor-methodical |downloads_bioconductor-methodical| |docker_bioconductor-methodical| :versions: ``1.6.0-0`` :depends on bioconductor-annotationhub: ``>=4.0.0,<4.1.0`` :depends on bioconductor-annotatr: ``>=1.36.0,<1.37.0`` :depends on bioconductor-bioccheck: ``>=1.46.0,<1.47.0`` :depends on bioconductor-biocparallel: ``>=1.44.0,<1.45.0`` :depends on bioconductor-biocstyle: ``>=2.38.0,<2.39.0`` :depends on bioconductor-biostrings: ``>=2.78.0,<2.79.0`` :depends on bioconductor-bsgenome: ``>=1.78.0,<1.79.0`` :depends on bioconductor-bsgenome.hsapiens.ucsc.hg19: ``>=1.4.0,<1.5.0`` :depends on bioconductor-bsgenome.hsapiens.ucsc.hg38: ``>=1.4.0,<1.5.0`` :depends on bioconductor-delayedarray: ``>=0.36.0,<0.37.0`` :depends on bioconductor-experimenthub: ``>=3.0.0,<3.1.0`` :depends on bioconductor-genomeinfodb: ``>=1.46.0,<1.47.0`` :depends on bioconductor-genomicranges: ``>=1.62.0,<1.63.0`` :depends on bioconductor-hdf5array: ``>=1.38.0,<1.39.0`` :depends on bioconductor-iranges: ``>=2.44.0,<2.45.0`` :depends on bioconductor-matrixgenerics: ``>=1.22.0,<1.23.0`` :depends on bioconductor-rhdf5: ``>=2.54.0,<2.55.0`` :depends on bioconductor-rtracklayer: ``>=1.70.0,<1.71.0`` :depends on bioconductor-s4vectors: ``>=0.48.0,<0.49.0`` :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0`` :depends on bioconductor-tumourmethdata: ``>=1.8.0,<1.9.0`` :depends on r-base: ``>=4.5,<4.6.0a0`` :depends on r-biocmanager: :depends on r-cowplot: :depends on r-data.table: :depends on r-devtools: :depends on r-dplyr: :depends on r-foreach: :depends on r-ggplot2: :depends on r-knitr: :depends on r-r.utils: :depends on r-rcmdcheck: :depends on r-rcpproll: :depends on r-remotes: :depends on r-scales: :depends on r-tibble: :depends on r-tidyr: :depends on r-usethis: :additional platforms: Installation ------------ You need a conda-compatible package manager (currently either `pixi `__, `conda `__, or `micromamba `__) and the Bioconda channel already activated (see :ref:`bioconda_setup`). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda). Pixi """" With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install globally, run:: pixi global install bioconductor-methodical to add into an existing workspace instead, run:: pixi add bioconductor-methodical In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:: pixi workspace channel add conda-forge pixi workspace channel add bioconda Conda """"" With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run:: conda install bioconductor-methodical Alternatively, to install into a new environment, run:: conda create -n envname bioconductor-methodical with ``envname`` being the name of the desired environment. Container """"""""" Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:: docker pull quay.io/biocontainers/bioconductor-methodical: (see `bioconductor-methodical/tags`_ for valid values for ````). Integrated deployment """"""""""""""""""""" Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration. .. _conda: https://conda.io .. _pixi: https://pixi.sh .. |downloads_bioconductor-methodical| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-methodical.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-methodical :alt: (downloads) .. |docker_bioconductor-methodical| image:: https://quay.io/repository/biocontainers/bioconductor-methodical/status :target: https://quay.io/repository/biocontainers/bioconductor-methodical .. _`bioconductor-methodical/tags`: https://quay.io/repository/biocontainers/bioconductor-methodical?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-methodical/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-methodical/README.html