recipe bioconductor-multicrispr

Multi-locus multi-purpose Crispr/Cas design

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-multicrispr/meta.yaml

This package is for designing Crispr/Cas9 and Prime Editing experiments. It contains functions to (1) define and transform genomic targets, (2) find spacers (4) count offtarget (mis)matches, and (5) compute Doench2016/2014 targeting efficiency. Care has been taken for multicrispr to scale well towards large target sets, enabling the design of large Crispr/Cas9 libraries.

package bioconductor-multicrispr

versions:

1.10.1-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

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-crisprseek:

>=1.40.0,<1.41.0

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-karyoploter:

>=1.26.0,<1.27.0

depends bioconductor-plyranges:

>=1.20.0,<1.21.0

depends bioconductor-rbowtie:

>=1.40.0,<1.41.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends r-assertive:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-ggplot2:

depends r-magrittr:

depends r-reticulate:

depends r-stringi:

depends r-tidyr:

depends r-tidyselect:

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-multicrispr

and update with::

   mamba update bioconductor-multicrispr

To create a new environment, run:

mamba create --name myenvname bioconductor-multicrispr

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-multicrispr:<tag>

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

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Link to this page

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