{ "_id": "6aea3ce19ceaa78f2009e12f", "Package": "IsoNetAnalyzeR", "Title": "Isoform-Level Protein Interaction Network Analysis", "Version": "0.99.0", "Authors@R": "c(\nperson(\"Dimitrios S.\", \"Kanakoglou\",\nemail = \"dimkan@dtu.dk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7735-2029\")),\nperson(\"Nikolas A.\", \"Mumm\",\nemail = \"s242825@dtu.dk\", role = \"aut\",\ncomment = c(ORCID = \"0009-0009-5751-0291\")),\nperson(\"Isabella\", \"Østerlund\", role = c(\"ctb\", \"ths\"),\ncomment = \"Isoform interaction model; protein-identical isoform map\"),\nperson(\"Kristoffer\", \"Vitting-Seerup\", role = c(\"cph\", \"ths\")),\nperson(\"Isoform Analysis Group\", role = \"cph\")\n)", "Description": "Compares predicted protein-interaction neighbourhoods of\ntranscript isoforms. The user supplies isoform seeds labelled\n\"up\" or \"down\", for example the isoforms that gain or lose\nusage in a differential transcript usage analysis. Each seed\nset is expanded in a bundled isoform-resolved predicted\ninteraction network, or in a user-supplied igraph network, and\nthe resulting neighbourhoods are compared per gene and\nsummarised across genes. The package also provides\nconnected-component analysis, network diagnostics, plots, and\nover-representation and gene set enrichment analysis of\nneighbourhood statistics. Protein-identical transcripts are\nresolved to shared representatives, and annotated\nnonsense-mediated and non-stop decay transcripts are excluded\nby default. Statistical testing of isoform usage remains\nupstream of the package.", "License": "MIT + file LICENSE", "URL": "https://github.com/IsoformAnalysisGroup/IsoNetAnalyzeR", "BugReports": "https://github.com/IsoformAnalysisGroup/IsoNetAnalyzeR/issues", "biocViews": "Software, Network, GraphAndNetwork, NetworkEnrichment,\nGeneSetEnrichment, AlternativeSplicing, DifferentialSplicing,\nTranscriptomics, SystemsBiology, Visualization", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Collate": "'isonetanalyzer_class.R' 'diff_pulldown_gene_class.R'\n'diff_pulldown_analysis_class.R' 'graph_utils.R'\n'component_analysis.R' 'duplicate_isoforms.R'\n'run_component_ora.R' 'run_fgsea.R' 'gsea_accessors.R'\n'lookup_class.R' 'lookup_vp.R' 'network_diagnostics_class.R'\n'plot_component.R' 'plot_diff_pulldown.R' 'plot_network.R'\n'plot_network_diagnostics.R' 'print_metadata.R'\n'run_differential_pulldown.R' 'run_network_diagnostics.R'\n'transcript_biotypes.R' 'virtual_pulldown.R'\n'virtual_pulldown_analysis.R'", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libxml2-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-11-03 12:36:09 UTC", "RemoteUrl": "https://github.com/BiocStaging/IsoNetAnalyzeR", "RemoteRef": "HEAD", "RemoteSha": "7197e6ff5d117f3c95792d104917eab67842aeb9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-03 19:51:53 UTC", "User": "root" }, "Author": "Dimitrios S. Kanakoglou [aut, cre] (ORCID:\n),\nNikolas A. Mumm [aut] (ORCID: ),\nIsabella Østerlund [ctb, ths] (Isoform interaction model;\nprotein-identical isoform map),\nKristoffer Vitting-Seerup [cph, ths],\nIsoform Analysis Group [cph]", "Maintainer": "Dimitrios S. Kanakoglou ", "_user": "biocstaging", "_type": "src", "_file": "IsoNetAnalyzeR_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/cf40375da111372eec101df4ae7e9acd2b94331c38707aced7a7340917e710a0", "_filesize": 3813272, "_sha256": "cf40375da111372eec101df4ae7e9acd2b94331c38707aced7a7340917e710a0", "_expires": "2027-02-11T19:58:23.000Z", "_created": "2026-11-03T19:51:53.000Z", "_published": "2026-11-03T19:58:25.559Z", "_upstream": "https://github.com/BiocStaging/IsoNetAnalyzeR", "_status": "success", "_maintainer": { "name": "Dimitrios S. 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