gemini

DOI: 10.18129/B9.bioc.gemini    

This is the development version of gemini; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

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 "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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Details

biocViews Bayesian, CRISPR, DataImport, Software
Version 0.99.11
In Bioconductor since BioC 3.10 (R-3.6)
License BSD_3_clause + file LICENSE
Depends R (>= 3.6.0)
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_0.99.11.tar.gz
Windows Binary gemini_0.99.11.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) gemini_0.99.11.tgz
Source Repository git clone https://git.bioconductor.org/packages/gemini
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gemini
Package Short Url https://bioconductor.org/packages/gemini/
Package Downloads Report Download Stats

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