Package Recipe 'bioconductor-gcrisprtools'

recipe bioconductor-gcrisprtools

Suite of Functions for Pooled Crispr Screen QC and Analysis

Homepage:: https://bioconductor.org/packages/3.20/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:

2.16.0-0, 2.12.0-0, 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,

2.16.0-0, 2.12.0-0, 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:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-ggplot2
on r-rmarkdown
on r-robustrankaggreg

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-gcrisprtools

to add into an existing workspace instead, run:

pixi add bioconductor-gcrisprtools

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-gcrisprtools

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gcrisprtools

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)