:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-motif2site' .. highlight: bash bioconductor-motif2site ======================= .. conda:recipe:: bioconductor-motif2site :replaces_section_title: :noindex: Detect binding sites from motifs and ChIP\-seq experiments\, and compare binding sites across conditions :homepage: https://bioconductor.org/packages/3.18/bioc/html/Motif2Site.html :license: GPL-2 :recipe: /`bioconductor-motif2site `_/`meta.yaml `_ Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP\-seq experiments in bed or bam format. Combine\/compare binding sites across experiments\, tissues\, or conditions. All normalization and differential steps are done using TMM\-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves. .. conda:package:: bioconductor-motif2site |downloads_bioconductor-motif2site| |docker_bioconductor-motif2site| :versions: ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicalignments: ``>=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-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-mass: :depends r-mixtools: :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-motif2site and update with:: mamba update bioconductor-motif2site To create a new environment, run:: mamba create --name myenvname bioconductor-motif2site 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-motif2site: (see `bioconductor-motif2site/tags`_ for valid values for ````) .. |downloads_bioconductor-motif2site| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-motif2site.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-motif2site :alt: (downloads) .. |docker_bioconductor-motif2site| image:: https://quay.io/repository/biocontainers/bioconductor-motif2site/status :target: https://quay.io/repository/biocontainers/bioconductor-motif2site .. _`bioconductor-motif2site/tags`: https://quay.io/repository/biocontainers/bioconductor-motif2site?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-motif2site/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-motif2site/README.html