This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see perturbatr.
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 (from within R,
enter citation("perturbatr")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("perturbatr")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("perturbatr")
HTML | R Script | perturbatr cookbook |
Reference Manual | ||
Text | NEWS |
biocViews | CellBasedAssays, ImmunoOncology, Network, Regression, Software |
Version | 1.4.0 |
In Bioconductor since | BioC 3.7 (R-3.5) (1.5 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 |
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 |
Package Short Url | https://bioconductor.org/packages/perturbatr/ |
Package Downloads Report | Download Stats |
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