perturbatr

DOI: 10.18129/B9.bioc.perturbatr    

Statistical Analysis of High-Throughput Genetic Perturbation Screens

Bioconductor version: Release (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("perturbatr")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("perturbatr")

 

HTML R Script perturbatr cookbook
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBasedAssays, Network, Regression, Software
Version 1.0.0
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 perturbatr_1.0.0.tar.gz
Windows Binary perturbatr_1.0.0.zip
Mac OS X 10.11 (El Capitan) perturbatr_1.0.0.tgz
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 http://bioconductor.org/packages/perturbatr/
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