gemini
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see gemini.
GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens
Bioconductor version: 3.11
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("gemini")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, CRISPR, DataImport, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| License | BSD_3_clause + file LICENSE |
| Depends | R (>= 3.6.0) |
| Imports | dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/sellerslab/gemini/issues |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gemini_1.2.0.tar.gz |
| Windows Binary | gemini_1.2.0.zip |
| macOS 10.13 (High Sierra) | gemini_1.2.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |