perturbatr

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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>

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

Installation

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


if (!require("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")
perturbatr cookbook HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, ImmunoOncology, Network, Regression, Software
Version 1.4.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL https://github.com/cbg-ethz/perturbatr
Bug Reports https://github.com/cbg-ethz/perturbatr/issues
See More
Suggests testthat, lintr, knitr, rmarkdown, BiocStyle
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 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
Bioc Package Browser https://code.bioconductor.org/browse/perturbatr/
Package Short Url https://bioconductor.org/packages/perturbatr/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive