:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-crisprbase' .. highlight: bash bioconductor-crisprbase ======================= .. conda:recipe:: bioconductor-crisprbase :replaces_section_title: :noindex: Base functions and classes for CRISPR gRNA design :homepage: https://bioconductor.org/packages/3.18/bioc/html/crisprBase.html :license: MIT + file LICENSE :recipe: /`bioconductor-crisprbase `_/`meta.yaml `_ Provides S4 classes for general nucleases\, CRISPR nucleases\, CRISPR nickases\, and base editors.Several CRISPR\-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly\-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA\- and RNA\-targeting nucleases are supported. .. conda:package:: bioconductor-crisprbase |downloads_bioconductor-crisprbase| |docker_bioconductor-crisprbase| :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-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-stringr: :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-crisprbase and update with:: mamba update bioconductor-crisprbase To create a new environment, run:: mamba create --name myenvname bioconductor-crisprbase 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-crisprbase: (see `bioconductor-crisprbase/tags`_ for valid values for ````) .. |downloads_bioconductor-crisprbase| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-crisprbase.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-crisprbase :alt: (downloads) .. |docker_bioconductor-crisprbase| image:: https://quay.io/repository/biocontainers/bioconductor-crisprbase/status :target: https://quay.io/repository/biocontainers/bioconductor-crisprbase .. _`bioconductor-crisprbase/tags`: https://quay.io/repository/biocontainers/bioconductor-crisprbase?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-crisprbase/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-crisprbase/README.html