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: 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

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
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
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: