recipe bioconductor-crisprbowtie

Bowtie-based alignment of CRISPR gRNA spacer sequences

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-crisprbowtie/meta.yaml

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported.

package bioconductor-crisprbowtie

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

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-crisprbase:

>=1.6.0,<1.7.0

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-rbowtie:

>=1.42.0,<1.43.0

depends r-base:

>=4.3,<4.4.0a0

depends r-readr:

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-crisprbowtie

and update with::

   mamba update bioconductor-crisprbowtie

To create a new environment, run:

mamba create --name myenvname bioconductor-crisprbowtie

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-crisprbowtie:<tag>

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

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Link to this page

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