recipe bioconductor-gcrisprtools

Suite of Functions for Pooled Crispr Screen QC and Analysis

Homepage:

https://bioconductor.org/packages/3.16/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:

2.4.0-0,  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, 

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 >=2.58.0,<2.59.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-rmarkdown

• r-robustrankaggreg

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-gcrisprtools

and update with:

conda update bioconductor-gcrisprtools

or use the docker container:

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

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

Download stats

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-gcrisprtools/README.html)