:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-dmrscan' .. highlight: bash bioconductor-dmrscan ==================== .. conda:recipe:: bioconductor-dmrscan :replaces_section_title: :noindex: Detection of Differentially Methylated Regions :homepage: https://bioconductor.org/packages/3.18/bioc/html/DMRScan.html :license: GPL-3 :recipe: /`bioconductor-dmrscan `_/`meta.yaml `_ This package detects significant differentially methylated regions \(for both qualitative and quantitative traits\)\, using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes \(\# of CpGs within each window\) and on a threshold for each window size. This threshold can be calculated by three different means\: i\) analytically using Siegmund et.al \(2012\) solution \(preferred\)\, ii\) an important sampling as suggested by Zhang \(2008\)\, and a iii\) full MCMC modeling of the data\, choosing between a number of different options for modeling the dependency between each CpG. .. conda:package:: bioconductor-dmrscan |downloads_bioconductor-dmrscan| |docker_bioconductor-dmrscan| :versions: .. raw:: html
1.24.0-01.22.0-01.20.0-01.16.0-01.14.0-01.12.0-11.12.0-01.11.0-01.10.0-1 ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.11.0-0``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0`` .. raw:: html
:depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-mass: :depends r-matrix: :depends r-mvtnorm: :depends r-rcpproll: :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-dmrscan and update with:: mamba update bioconductor-dmrscan To create a new environment, run:: mamba create --name myenvname bioconductor-dmrscan 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-dmrscan: (see `bioconductor-dmrscan/tags`_ for valid values for ````) .. |downloads_bioconductor-dmrscan| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-dmrscan.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-dmrscan :alt: (downloads) .. |docker_bioconductor-dmrscan| image:: https://quay.io/repository/biocontainers/bioconductor-dmrscan/status :target: https://quay.io/repository/biocontainers/bioconductor-dmrscan .. _`bioconductor-dmrscan/tags`: https://quay.io/repository/biocontainers/bioconductor-dmrscan?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-dmrscan/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-dmrscan/README.html