Package Recipe 'bioconductor-gcrisprtools'

recipe bioconductor-gcrisprtools

Suite of Functions for Pooled Crispr Screen QC and Analysis

Homepage: https://bioconductor.org/packages/3.14/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

2.0.0-0, 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,

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 >=2.54.0,<2.55.0
bioconductor-complexheatmap >=2.10.0,<2.11.0
bioconductor-limma >=3.50.0,<3.51.0
bioconductor-summarizedexperiment >=1.24.0,<1.25.0
r-base >=4.1,<4.2.0a0
r-ggplot2
r-rmarkdown
r-robustrankaggreg

Required By

Installation

With an activated Bioconda channel (see 2. 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)