perturbatr
This package is for version 3.9 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: 3.9
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 "3.6") 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, ImmunoOncology, Network, Regression, Software |
| Version | 1.4.0 |
| 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_1.4.0.tar.gz |
| Windows Binary | perturbatr_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | perturbatr_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/perturbatr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/perturbatr |
| Bioc Package Browser | https://code.bioconductor.org/browse/perturbatr/ |
| Package Short Url | https://bioconductor.org/packages/perturbatr/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |