recipe bioconductor-crisprseek

The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. This package leverages Biostrings and BSgenome packages.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/CRISPRseek.html

License

GPL (>= 2)

Recipe

/bioconductor-crisprseek/meta.yaml

Links

biotools: crisprseek

package bioconductor-crisprseek

Versions

1.24.0-1, 1.22.0-0, 1.20.0-0, 1.18.0-0

Depends

• bioconductor-biocgenerics >=0.30.0,<0.31.0

• bioconductor-biocparallel >=1.18.0,<1.19.0

• bioconductor-biostrings >=2.52.0,<2.53.0

• bioconductor-bsgenome >=1.52.0,<1.53.0

• bioconductor-iranges >=2.18.0,<2.19.0

• bioconductor-s4vectors >=0.22.0,<0.23.0

• r-base >=3.6,<3.7.0a0

• r-data.table

• r-hash

• r-seqinr

Required By

• bioconductor-crisprseekplus

• bioconductor-guideseq

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-crisprseek

and update with:

conda update bioconductor-crisprseek

or use the docker container:

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

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

Link to this page

Render an 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-crisprseek/README.html)