:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-genomicfeatures' .. highlight: bash bioconductor-genomicfeatures ============================ .. conda:recipe:: bioconductor-genomicfeatures :replaces_section_title: :noindex: Conveniently import and query gene models :homepage: https://bioconductor.org/packages/3.18/bioc/html/GenomicFeatures.html :license: Artistic-2.0 :recipe: /`bioconductor-genomicfeatures `_/`meta.yaml `_ :links: biotools: :biotools:`genomicfeatures` A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts\, exons and cds of a given organism\, from either the UCSC Genome Browser or a BioMart database \(more sources will be supported in the future\). This information is then stored in a local database that keeps track of the relationship between transcripts\, exons\, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format. .. conda:package:: bioconductor-genomicfeatures |downloads_bioconductor-genomicfeatures| |docker_bioconductor-genomicfeatures| :versions: .. raw:: html
1.54.1-01.52.1-01.50.2-01.46.1-01.44.0-01.42.2-01.42.0-01.40.0-01.38.0-0 ``1.54.1-0``,  ``1.52.1-0``,  ``1.50.2-0``,  ``1.46.1-0``,  ``1.44.0-0``,  ``1.42.2-0``,  ``1.42.0-0``,  ``1.40.0-0``,  ``1.38.0-0``,  ``1.36.4-0``,  ``1.36.0-0``,  ``1.34.1-0``,  ``1.32.3-0``,  ``1.30.3-0``,  ``1.30.0-0``,  ``1.28.5-0``,  ``1.26.4-0``,  ``1.26.0-2``,  ``1.24.5-2``,  ``1.24.5-1``,  ``1.24.5-0``,  ``1.22.13-0``,  ``1.22.6-0``,  ``1.22.4-0``,  ``1.22.0-0`` .. raw:: html
:depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocio: ``>=1.12.0,<1.13.0`` :depends bioconductor-biomart: ``>=2.58.0,<2.59.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :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 bioconductor-xvector: ``>=0.42.0,<0.43.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dbi: :depends r-rcurl: :depends r-rsqlite: ``>=2.0`` :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-genomicfeatures and update with:: mamba update bioconductor-genomicfeatures To create a new environment, run:: mamba create --name myenvname bioconductor-genomicfeatures 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-genomicfeatures: (see `bioconductor-genomicfeatures/tags`_ for valid values for ````) .. |downloads_bioconductor-genomicfeatures| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-genomicfeatures.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-genomicfeatures :alt: (downloads) .. |docker_bioconductor-genomicfeatures| image:: https://quay.io/repository/biocontainers/bioconductor-genomicfeatures/status :target: https://quay.io/repository/biocontainers/bioconductor-genomicfeatures .. _`bioconductor-genomicfeatures/tags`: https://quay.io/repository/biocontainers/bioconductor-genomicfeatures?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-genomicfeatures/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-genomicfeatures/README.html