:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-motifcounter' .. highlight: bash bioconductor-motifcounter ========================= .. conda:recipe:: bioconductor-motifcounter :replaces_section_title: :noindex: R package for analysing TFBSs in DNA sequences :homepage: https://bioconductor.org/packages/3.18/bioc/html/motifcounter.html :license: GPL-2 :recipe: /`bioconductor-motifcounter `_/`meta.yaml `_ \'motifcounter\' provides motif matching\, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higher\-order background models and accounting for self\-overlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide \(or higher\-order nucleotide\) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count\, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for self\-overlapping motif structures as exemplified by repeat\-like or palindromic motifs\, and allow to determine the p\-value and fold\-enrichment for a set of observed motif matches. .. conda:package:: bioconductor-motifcounter |downloads_bioconductor-motifcounter| |docker_bioconductor-motifcounter| :versions: .. raw:: html
1.26.0-01.24.0-01.22.0-11.22.0-01.18.0-21.18.0-11.18.0-01.16.0-01.14.0-1 ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.18.0-2``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.1-0`` .. raw:: html
:depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends r-base: ``>=4.3,<4.4.0a0`` :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-motifcounter and update with:: mamba update bioconductor-motifcounter To create a new environment, run:: mamba create --name myenvname bioconductor-motifcounter 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-motifcounter: (see `bioconductor-motifcounter/tags`_ for valid values for ````) .. |downloads_bioconductor-motifcounter| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-motifcounter.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-motifcounter :alt: (downloads) .. |docker_bioconductor-motifcounter| image:: https://quay.io/repository/biocontainers/bioconductor-motifcounter/status :target: https://quay.io/repository/biocontainers/bioconductor-motifcounter .. _`bioconductor-motifcounter/tags`: https://quay.io/repository/biocontainers/bioconductor-motifcounter?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-motifcounter/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-motifcounter/README.html