gemini

DOI: 10.18129/B9.bioc.gemini  

GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

Bioconductor version: Release (3.16)

GEMINI uses log-fold changes to model sample-dependent and independent effects, and uses a variational Bayes approach to infer these effects. The inferred effects are used to score and identify genetic interactions, such as lethality and recovery. More details can be found in Zamanighomi et al. 2019 (in press).

Author: Mahdi Zamanighomi [aut], Sidharth Jain [aut, cre]

Maintainer: Sidharth Jain <sidharthsjain at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gemini")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("gemini")

 

HTML	R Script	QuickStart
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, CRISPR, DataImport, Software
Version	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
License	BSD_3_clause + file LICENSE
Depends	R (>= 4.1.0)
Imports	dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/sellerslab/gemini/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	gemini_1.12.0.tar.gz
Windows Binary	gemini_1.12.0.zip
macOS Binary (x86_64)	gemini_1.12.0.tgz
macOS Binary (arm64)	gemini_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gemini
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gemini
Bioc Package Browser	https://code.bioconductor.org/browse/gemini/
Package Short Url	https://bioconductor.org/packages/gemini/
Package Downloads Report	Download Stats