:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-annmap' .. highlight: bash bioconductor-annmap =================== .. conda:recipe:: bioconductor-annmap :replaces_section_title: :noindex: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis. :homepage: https://bioconductor.org/packages/3.18/bioc/html/annmap.html :license: GPL-2 :recipe: /`bioconductor-annmap `_/`meta.yaml `_ :links: biotools: :biotools:`annmap`, doi: :doi:`10.1093/nar/gkm779` annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange\(\)\, geneToExon\(\)\, exonDetails\(\)\, etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from\: https\:\/\/figshare.manchester.ac.uk\/account\/articles\/16685071 .. conda:package:: bioconductor-annmap |downloads_bioconductor-annmap| |docker_bioconductor-annmap| :versions: .. raw:: html
1.44.0-01.42.0-01.40.0-01.36.0-01.34.0-01.32.0-11.32.0-01.30.0-01.28.0-0 ``1.44.0-0``,  ``1.42.0-0``,  ``1.40.0-0``,  ``1.36.0-0``,  ``1.34.0-0``,  ``1.32.0-1``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-1``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-genefilter: ``>=1.84.0,<1.85.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dbi: :depends r-digest: :depends r-lattice: :depends r-rmysql: ``>=0.6-0`` :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-annmap and update with:: mamba update bioconductor-annmap To create a new environment, run:: mamba create --name myenvname bioconductor-annmap 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-annmap: (see `bioconductor-annmap/tags`_ for valid values for ````) .. |downloads_bioconductor-annmap| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-annmap.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-annmap :alt: (downloads) .. |docker_bioconductor-annmap| image:: https://quay.io/repository/biocontainers/bioconductor-annmap/status :target: https://quay.io/repository/biocontainers/bioconductor-annmap .. _`bioconductor-annmap/tags`: https://quay.io/repository/biocontainers/bioconductor-annmap?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-annmap/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-annmap/README.html