recipe bioconductor-gcrisprtools

Suite of Functions for Pooled Crispr Screen QC and Analysis

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-gcrisprtools/meta.yaml

Links:

biotools: gcrisprtools, doi: 10.1038/nmeth.3252

Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.

package bioconductor-gcrisprtools

versions:

2.8.0-0,  2.6.0-0,  2.4.0-0,  2.0.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0, 

2.8.0-0,  2.6.0-0,  2.4.0-0,  2.0.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-rmarkdown:

depends r-robustrankaggreg:

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-gcrisprtools

and update with::

   mamba update bioconductor-gcrisprtools

To create a new environment, run:

mamba create --name myenvname bioconductor-gcrisprtools

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-gcrisprtools:<tag>

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

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