Package Recipe 'bioconductor-mageckflute'

recipe bioconductor-mageckflute

Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/MAGeCKFlute.html
License:: GPL (>=3)
Recipe:: /bioconductor-mageckflute/meta.yaml

CRISPR (clustered regularly interspaced short palindrome repeats) coupled with nuclease Cas9 (CRISPR/Cas9) screens represent a promising technology to systematically evaluate gene functions. Data analysis for CRISPR/Cas9 screens is a critical process that includes identifying screen hits and exploring biological functions for these hits in downstream analysis. We have previously developed two algorithms, MAGeCK and MAGeCK-VISPR, to analyze CRISPR/Cas9 screen data in various scenarios. These two algorithms allow users to perform quality control, read count generation and normalization, and calculate beta score to evaluate gene selection performance. In downstream analysis, the biological functional analysis is required for understanding biological functions of these identified genes with different screening purposes. Here, We developed MAGeCKFlute for supporting downstream analysis. MAGeCKFlute provides several strategies to remove potential biases within sgRNA-level read counts and gene-level beta scores. The downstream analysis with the package includes identifying essential, non-essential, and target-associated genes, and performing biological functional category analysis, pathway enrichment analysis and protein complex enrichment analysis of these genes. The package also visualizes genes in multiple ways to benefit users exploring screening data. Collectively, MAGeCKFlute enables accurate identification of essential, non-essential, and targeted genes, as well as their related biological functions. This vignette explains the use of the package and demonstrates typical workflows.

package bioconductor-mageckflute¶

Versions:

2.9.0-0, 2.6.0-0, 2.4.0-0, 2.2.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0,

2.9.0-0, 2.6.0-0, 2.4.0-0, 2.2.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.2-0, 1.2.3-0, 1.2.2-0

Depends:

on bioconductor-biobase >=2.66.0,<2.67.0
on bioconductor-clusterprofiler >=4.14.0,<4.15.0
on bioconductor-depmap >=1.20.0,<1.21.0
on bioconductor-dose >=4.0.0,<4.1.0
on bioconductor-enrichplot >=1.26.0,<1.27.0
on bioconductor-pathview >=1.46.0,<1.47.0
on r-base >=4.4,<4.5.0a0
on r-ggplot2
on r-ggrepel
on r-gridextra
on r-msigdbr
on r-reshape2

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-mageckflute

to add into an existing workspace instead, run:

pixi add bioconductor-mageckflute

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-mageckflute

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mageckflute

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-mageckflute:<tag>

(see bioconductor-mageckflute/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-mageckflute/README.html)