recipe bioconductor-crisprscore

On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/crisprScore.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-crisprscore/meta.yaml

Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.

package bioconductor-crisprscore

versions:

1.4.0-0,  1.2.0-0

depends bioconductor-basilisk:

>=1.12.0,<1.13.0

depends bioconductor-basilisk.utils:

>=1.12.0,<1.13.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-crisprscoredata:

>=1.4.0,<1.5.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-xvector:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-randomforest:

depends r-reticulate:

depends r-stringr:

requirements:

Installation

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-crisprscore

and update with::

   mamba update bioconductor-crisprscore

To create a new environment, run:

mamba create --name myenvname bioconductor-crisprscore

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-crisprscore:<tag>

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

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