perturbatr

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.15 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: 3.15

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 "4.2") 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

Details

biocViews CellBasedAssays, ImmunoOncology, Network, Regression, Software
Version 1.16.0
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
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
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 3.15 Source Archive