recipe bioconductor-crisprdesign

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-crisprdesign/meta.yaml

Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

package bioconductor-crisprdesign

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-bsgenome:

>=1.68.0,<1.69.0

depends bioconductor-crisprbase:

>=1.4.0,<1.5.0

depends bioconductor-crisprbowtie:

>=1.4.0,<1.5.0

depends bioconductor-crisprscore:

>=1.4.0,<1.5.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-matrixgenerics:

>=1.12.0,<1.13.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

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-crisprdesign

and update with::

   mamba update bioconductor-crisprdesign

To create a new environment, run:

mamba create --name myenvname bioconductor-crisprdesign

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-crisprdesign:<tag>

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

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Link to this page

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