perturbatr

DOI: 10.18129/B9.bioc.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: Release (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>

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

PDF		Reference Manual

Details

biocViews	CellBasedAssays, ImmunoOncology, Network, Regression, Software
Version	1.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 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
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Imports Me
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Build Report

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/
Package Downloads Report	Download Stats