perturbatr

DOI: 10.18129/B9.bioc.perturbatr    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see perturbatr.

Statistical Analysis of High-Throughput Genetic Perturbation Screens

Bioconductor version: 3.9

perturbatr does stage-wise analysis of large-scale genetic perturbation screens for integrated data sets consisting of multiple screens. For multiple integrated perturbation screens a hierarchical model that considers the variance between different biological conditions is fitted. The resulting list of gene effects is then further extended using a network propagation algorithm to correct for false negatives.

Author: Simon Dirmeier [aut, cre]

Maintainer: Simon Dirmeier <simon.dirmeier at web.de>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("perturbatr")

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("perturbatr")

 

HTML	R Script	perturbatr cookbook
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, ImmunoOncology, Network, Regression, Software
Version	1.4.0
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
License	GPL-3
Depends	R (>= 3.5), methods, stats
Imports	dplyr, ggplot2, tidyr, assertthat, lme4, splines, igraph, foreach, parallel, doParallel, diffusr, lazyeval, tibble, grid, utils, graphics, scales, magrittr, formula.tools, rlang
LinkingTo
Suggests	testthat, lintr, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/cbg-ethz/perturbatr
BugReports	https://github.com/cbg-ethz/perturbatr/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	perturbatr_1.4.0.tar.gz
Windows Binary	perturbatr_1.4.0.zip
Mac OS X 10.11 (El Capitan)	perturbatr_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/perturbatr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/perturbatr
Package Short Url	https://bioconductor.org/packages/perturbatr/
Package Downloads Report	Download Stats