perturbatr
This package is for version 3.7 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: 3.7
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("perturbatr")
):
Installation
To install this package, start R (version "3.5") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("perturbatr")
perturbatr cookbook | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | CellBasedAssays, Network, Regression, Software |
Version | 1.0.0 |
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 |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | 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 | https://bioconductor.org/packages/perturbatr/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.7 | Source Archive |