recipe bioconductor-crisprseek

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/CRISPRseek.html

License:

GPL (>= 2)

Recipe:

/bioconductor-crisprseek/meta.yaml

Links:

biotools: crisprseek

The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor 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. The package also output indels and their frequencies for Cas9 targeted sites.

package bioconductor-crisprseek

versions:

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.1-0,  1.30.0-0,  1.28.0-0,  1.26.0-0, 

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.1-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rhdf5:

>=2.46.0,<2.47.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-xvector:

>=0.42.0,<0.43.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-hash:

depends r-keras:

depends r-mltools:

depends r-reticulate:

depends r-seqinr:

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-crisprseek

and update with::

   mamba update bioconductor-crisprseek

To create a new environment, run:

mamba create --name myenvname bioconductor-crisprseek

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-crisprseek:<tag>

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

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