{"id":20751276,"url":"https://github.com/cbg-ethz/perturbatr","last_synced_at":"2026-05-25T04:32:14.124Z","repository":{"id":133194211,"uuid":"63546121","full_name":"cbg-ethz/perturbatr","owner":"cbg-ethz","description":"Analysis of high-throughput genetic perturbation screens in 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perturbatr \u003cimg src=\"https://rawgit.com/cbg-ethz/perturbatr/master/inst/figure/sticker.png\" align=\"right\" width=\"160px\"/\u003e\n\n[![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n[![Build Status](https://travis-ci.org/cbg-ethz/perturbatr.svg?branch=master)](https://travis-ci.org/cbg-ethz/perturbatr)\n[![Build app](https://ci.appveyor.com/api/projects/status/a28cs08ug9qng8hn?svg=true)](https://ci.appveyor.com/project/dirmeier/perturbatr)\n[![codecov](https://codecov.io/gh/cbg-ethz/perturbatr/branch/master/graph/badge.svg)](https://codecov.io/gh/cbg-ethz/perturbatr)\n[![bioc](https://bioconductor.org/shields/years-in-bioc/perturbatr.svg)](https://bioconductor.org/packages/release/bioc/html/perturbatr.html)\n\nAnalysis of high-throughput gene perturbation screens in R.\n\n## Introduction\n\n`perturbatr` does stage-wise analysis of large-scale genetic\nperturbation screens for integrated data sets consisting of multiple screens.\nFor multiple integrated perturbation screens a hierarchical model that\nconsiders the variance between different biological conditions is fitted.\nThat means that we first estimate relative effect sizes for all genes.\nThe resulting hit lists is then further extended using a network\npropagation algorithm to correct for false negatives. and positives.\n\n```{r}\ndata(rnaiscreen)\ngraph \u003c- readRDS(\n  system.file(\"extdata\", \"graph_file.tsv\", package = \"perturbatr\"))\n\nfrm   \u003c- Readout ~ Condition +\n                   (1|GeneSymbol) + (1|Condition:GeneSymbol) +\n                   (1|ScreenType) + (1|Condition:ScreenType)\nft    \u003c- hm(rnaiscreen, formula = frm)\ndiffu \u003c- diffuse(ft, graph=graph, r=0.3)\n\nplot(diffu)\n```\n\n## Installation\n\nYou can install and use `perturbatr` either as an `R` library from [Bioconductor](https://doi.org/doi:10.18129/B9.bioc.perturbatr),\nor by downloading the [tarball](https://github.com/cbg-ethz/perturbatr/releases).\n\nIf you want to use the **recommended** way using Bioconductor just call:\n\n```r\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n  install.packages(\"BiocManager\")\nBiocManager::install(\"perturbatr\")\n  \nlibrary(perturbatr)\n```\n\nfrom the R-console.\n\nInstalling the package using the downloaded tarball works like this:\n\n```bash\n  R CMD install \u003cperturbatr.tar.gz\u003e\n```\n\nwhere `perturbatr.tar.gz` is the downloaded tarball.\n\n## Documentation\n\nLoad the package using `library(perturbatr)`. We provide a vignette for the package that can be called using: `vignette(\"perturbatr\")`.\n\n## Author\n\n* Simon Dirmeier \u003ca href=\"mailto:simon.dirmeier@bsse.ethz.ch\"\u003esimon.dirmeier@bsse.ethz.ch\u003c/a\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fperturbatr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbg-ethz%2Fperturbatr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fperturbatr/lists"}