Package: MSstatsBioNet Type: Package Title: Network Analysis for MS-based Proteomics Experiments Version: 1.5.5 Authors@R: c( person("Anthony", "Wu", email = "wu.anthon@northeastern.edu", role = c("aut", "cre"), comment = c(ORCID = "0009-0001-7391-9902")), person("Olga", "Vitek", email = "o.vitek@northeastern.edu", role = "aut", comment=c(ORCID = "0000-0003-1728-1104"))) Description: A set of tools for network analysis using mass spectrometry-based proteomics data and network databases. The package takes as input the output of MSstats differential abundance analysis and provides functions to perform enrichment analysis and visualization in the context of prior knowledge from past literature. Notably, this package integrates with INDRA, which is a database of biological networks extracted from the literature using text mining techniques. License: file LICENSE Depends: R (>= 4.4.0), MSstats Imports: httr, jsonlite, r2r, tidyr, htmlwidgets, grDevices, stats, text2vec, stopwords, xml2, rentrez, methods Suggests: data.table, BiocStyle, knitr, rmarkdown, testthat (>= 3.1.7), mockery, MSstatsConvert, shiny VignetteBuilder: knitr biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, QualityControl, NetworkEnrichment, Network Encoding: UTF-8 URL: http://msstats.org, https://vitek-lab.github.io/MSstatsBioNet/ BugReports: https://groups.google.com/forum/#!forum/msstats Config/testthat/edition: 3 Config/roxygen2/version: 8.1.0 Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libxml2-dev libssl-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-10-23 14:27:02 UTC RemoteUrl: https://github.com/bioc/MSstatsBioNet RemoteRef: HEAD RemoteSha: a9e97749a7cd72fd6533b0194c4fcf6d4f4b0058 NeedsCompilation: no Packaged: 2026-10-23 18:43:59 UTC; root Author: Anthony Wu [aut, cre] (ORCID: ), Olga Vitek [aut] (ORCID: ) Maintainer: Anthony Wu