:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-multicrispr' .. highlight: bash bioconductor-multicrispr ======================== .. conda:recipe:: bioconductor-multicrispr :replaces_section_title: :noindex: Multi\-locus multi\-purpose Crispr\/Cas design :homepage: https://bioconductor.org/packages/3.18/bioc/html/multicrispr.html :license: GPL-2 :recipe: /`bioconductor-multicrispr `_/`meta.yaml `_ This package is for designing Crispr\/Cas9 and Prime Editing experiments. It contains functions to \(1\) define and transform genomic targets\, \(2\) find spacers \(4\) count offtarget \(mis\)matches\, and \(5\) compute Doench2016\/2014 targeting efficiency. Care has been taken for multicrispr to scale well towards large target sets\, enabling the design of large Crispr\/Cas9 libraries. .. conda:package:: bioconductor-multicrispr |downloads_bioconductor-multicrispr| |docker_bioconductor-multicrispr| :versions: ``1.12.3-0``,  ``1.10.1-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-2``,  ``1.0.0-1`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-crisprseek: ``>=1.42.0,<1.43.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-karyoploter: ``>=1.28.0,<1.29.0`` :depends bioconductor-plyranges: ``>=1.22.0,<1.23.0`` :depends bioconductor-rbowtie: ``>=1.42.0,<1.43.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends r-assertive.base: :depends r-assertive.files: :depends r-assertive.numbers: :depends r-assertive.reflection: :depends r-assertive.sets: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-ggplot2: :depends r-magrittr: :depends r-reticulate: :depends r-stringi: :depends r-tidyr: :depends r-tidyselect: :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-multicrispr and update with:: mamba update bioconductor-multicrispr To create a new environment, run:: mamba create --name myenvname bioconductor-multicrispr 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-multicrispr: (see `bioconductor-multicrispr/tags`_ for valid values for ````) .. |downloads_bioconductor-multicrispr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-multicrispr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-multicrispr :alt: (downloads) .. |docker_bioconductor-multicrispr| image:: https://quay.io/repository/biocontainers/bioconductor-multicrispr/status :target: https://quay.io/repository/biocontainers/bioconductor-multicrispr .. _`bioconductor-multicrispr/tags`: https://quay.io/repository/biocontainers/bioconductor-multicrispr?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-multicrispr/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-multicrispr/README.html