:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-periodicdna' .. highlight: bash bioconductor-periodicdna ======================== .. conda:recipe:: bioconductor-periodicdna :replaces_section_title: :noindex: Set of tools to identify periodic occurrences of k\-mers in DNA sequences :homepage: https://bioconductor.org/packages/3.18/bioc/html/periodicDNA.html :license: GPL-3 + file LICENSE :recipe: /`bioconductor-periodicdna `_/`meta.yaml `_ This R package helps the user identify k\-mers \(e.g. di\- or tri\-nucleotides\) present periodically in a set of genomic loci \(typically regulatory elements\). The functions of this package provide a straightforward approach to find periodic occurrences of k\-mers in DNA sequences\, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance\; for this type of analysis\, please visit MEME website. .. conda:package:: bioconductor-periodicdna |downloads_bioconductor-periodicdna| |docker_bioconductor-periodicdna| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-2``,  ``1.0.0-1`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :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 bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-cowplot: :depends r-ggplot2: :depends r-magrittr: :depends r-zoo: :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-periodicdna and update with:: mamba update bioconductor-periodicdna To create a new environment, run:: mamba create --name myenvname bioconductor-periodicdna 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-periodicdna: (see `bioconductor-periodicdna/tags`_ for valid values for ````) .. |downloads_bioconductor-periodicdna| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-periodicdna.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-periodicdna :alt: (downloads) .. |docker_bioconductor-periodicdna| image:: https://quay.io/repository/biocontainers/bioconductor-periodicdna/status :target: https://quay.io/repository/biocontainers/bioconductor-periodicdna .. _`bioconductor-periodicdna/tags`: https://quay.io/repository/biocontainers/bioconductor-periodicdna?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-periodicdna/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-periodicdna/README.html