{ "_id": "6aafa9943d719c1f840806ce", "Package": "DEP", "Title": "Differential Enrichment analysis of Proteomics data", "Version": "3.99.0", "Authors@R": "c(\nperson(\"Jelmer\", \"Dijkstra\", email = \"protechrobioMV@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Arne\", \"Smits\", email = \"smits.arne@gmail.com\", role = \"aut\"),\nperson(\"Wolfgang\", \"Huber\", email = \"wolfgang.huber@embl.de\", role = \"aut\"))", "Description": "This package provides an integrated analysis workflow for\nrobust and reproducible analysis of mass spectrometry\nproteomics data for differential protein expression or\ndifferential enrichment. It requires tabular input (e.g. txt\nfiles) as generated by quantitative analysis softwares of raw\nmass spectrometry data, such as MaxQuant or IsobarQuant.\nFunctions are provided for data preparation, filtering,\nvariance normalization and imputation of missing values, as\nwell as statistical testing of differentially enriched /\nexpressed proteins. It also includes tools to check\nintermediate steps in the workflow, such as normalization and\nmissing values imputation. Finally, visualization tools are\nprovided to explore the results, including heatmap, volcano\nplot and barplot representations. For scientists with limited\nexperience in R, the package also contains wrapper functions\nthat entail the complete analysis workflow and generate a\nreport. Even easier to use are the interactive Shiny apps that\nare provided by the package.", "License": "Artistic-2.0", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "ImmunoOncology, Proteomics, MassSpectrometry,\nDifferentialExpression, DataRepresentation", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libnetcdf-dev libssl-dev perl libx11-dev\nzlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-08-21 12:21:23 UTC", "RemoteUrl": "https://github.com/BiocStaging/DEP", "RemoteRef": "HEAD", "RemoteSha": "c83f65987ca9787619c998ef654c07a110e2ec1a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-20 09:30:15 UTC", "User": "root" }, "Author": "Jelmer Dijkstra [aut, cre],\nArne Smits [aut],\nWolfgang Huber [aut]", "Maintainer": "Jelmer Dijkstra ", "_user": "biocstaging", "_type": "src", "_file": "DEP_3.99.0.tar.gz", "_fileid": 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