recipe bioconductor-crisprbase

Base functions and classes for CRISPR gRNA design






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.

package bioconductor-crisprbase

(downloads) docker_bioconductor-crisprbase



depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends r-base:


depends r-stringr:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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<tag>

(see `bioconductor-crisprbase/tags`_ for valid values for ``<tag>``)

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