recipe bioconductor-crisprdesign

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Homepage:

https://bioconductor.org/packages/3.16/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:

1.0.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-crisprbase >=1.2.0,<1.3.0

• bioconductor-crisprbowtie >=1.2.0,<1.3.0

• bioconductor-crisprscore >=1.2.0,<1.3.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-matrixgenerics >=1.10.0,<1.11.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-variantannotation >=1.44.0,<1.45.0

• r-base >=4.2,<4.3.0a0

• r-matrix

Required By:

• bioconductor-crisprverse

• bioconductor-crisprviz

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-crisprdesign

and update with:

conda update bioconductor-crisprdesign

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-crisprdesign:<tag>

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

Download stats

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