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gemini

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("gemini")):

Installation

To install this package, start R (version "4.3") 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")
QuickStart HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Bayesian, CRISPR, DataImport, Software
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License BSD_3_clause + file LICENSE
Depends R (>= 4.1.0)
Imports dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils
System Requirements
URL
Bug Reports https://github.com/sellerslab/gemini/issues
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Suggests knitr, rmarkdown, testthat
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Package Archives

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

Source Package gemini_1.16.0.tar.gz
Windows Binary gemini_1.16.0.zip (64-bit only)
macOS Binary (x86_64) gemini_1.16.0.tgz
macOS Binary (arm64) gemini_1.16.0.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/
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