:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-biocio' .. highlight: bash bioconductor-biocio =================== .. conda:recipe:: bioconductor-biocio :replaces_section_title: :noindex: Standard Input and Output for Bioconductor Packages :homepage: https://bioconductor.org/packages/3.18/bioc/html/BiocIO.html :license: Artistic-2.0 :recipe: /`bioconductor-biocio `_/`meta.yaml `_ The \`BiocIO\` package contains high\-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements \`import\(\)\` and \`export\(\)\` standard generics for importing and exporting biological data formats. \`import\(\)\` supports whole\-file as well as chunk\-wise iterative import. The \`import\(\)\` interface optionally provides a standard mechanism for \'lazy\' access via \`filter\(\)\` \(on row or element\-like components of the file resource\)\, \`select\(\)\` \(on column\-like components of the file resource\) and \`collect\(\)\`. The \`import\(\)\` interface optionally provides transparent access to remote \(e.g. via https\) as well as local access. Developers can register a file extension\, e.g.\, \`.loom\` for dispatch from character\-based URIs to specific \`import\(\)\` \/ \`export\(\)\` methods based on classes representing file types\, e.g.\, \`LoomFile\(\)\`. .. conda:package:: bioconductor-biocio |downloads_bioconductor-biocio| |docker_bioconductor-biocio| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.1-0``,  ``1.0.0-1`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :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-biocio and update with:: mamba update bioconductor-biocio To create a new environment, run:: mamba create --name myenvname bioconductor-biocio 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-biocio: (see `bioconductor-biocio/tags`_ for valid values for ````) .. |downloads_bioconductor-biocio| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-biocio.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-biocio :alt: (downloads) .. |docker_bioconductor-biocio| image:: https://quay.io/repository/biocontainers/bioconductor-biocio/status :target: https://quay.io/repository/biocontainers/bioconductor-biocio .. _`bioconductor-biocio/tags`: https://quay.io/repository/biocontainers/bioconductor-biocio?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-biocio/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-biocio/README.html