perturbatr

This package is for version 3.14 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

DOI: 10.18129/B9.bioc.perturbatr

Bioconductor version: 3.14

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 "4.1") 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

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, ImmunoOncology, Network, Regression, Software

Version 1.14.0

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

Suggests testthat, lintr, knitr, rmarkdown, BiocStyle

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Package Archives

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

Source Package

Windows Binary

macOS 10.13 (High Sierra)

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/

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Old Source Packages for BioC 3.14 Source Archive