Package: IsoNetAnalyzeR
Title: Isoform-Level Protein Interaction Network Analysis
Version: 0.99.0
Authors@R: c(
    person("Dimitrios S.", "Kanakoglou",
           email = "dimkan@dtu.dk", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-7735-2029")),
    person("Nikolas A.", "Mumm",
           email = "s242825@dtu.dk", role = "aut",
           comment = c(ORCID = "0009-0009-5751-0291")),
    person("Isabella", "Østerlund", role = c("ctb", "ths"),
           comment = "Isoform interaction model; protein-identical isoform map"),
    person("Kristoffer", "Vitting-Seerup", role = c("cph", "ths")),
    person("Isoform Analysis Group", role = "cph")
    )
Description: Compares predicted protein-interaction neighbourhoods of
        transcript isoforms. The user supplies isoform seeds labelled
        "up" or "down", for example the isoforms that gain or lose
        usage in a differential transcript usage analysis. Each seed
        set is expanded in a bundled isoform-resolved predicted
        interaction network, or in a user-supplied igraph network, and
        the resulting neighbourhoods are compared per gene and
        summarised across genes. The package also provides
        connected-component analysis, network diagnostics, plots, and
        over-representation and gene set enrichment analysis of
        neighbourhood statistics. Protein-identical transcripts are
        resolved to shared representatives, and annotated
        nonsense-mediated and non-stop decay transcripts are excluded
        by default. Statistical testing of isoform usage remains
        upstream 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,
        GeneSetEnrichment, AlternativeSplicing, DifferentialSplicing,
        Transcriptomics, SystemsBiology, Visualization
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.5.0)
Imports: methods, igraph, cli, stats, utils, ggplot2, ggraph,
        patchwork, rlang, fgsea, future, future.apply, ggrepel,
        progressr, withr
Suggests: BiocStyle, knitr, rmarkdown, msigdbr, colorspace, readxl,
        SummarizedExperiment, S4Vectors, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Collate: 'isonetanalyzer_class.R' 'diff_pulldown_gene_class.R'
        'diff_pulldown_analysis_class.R' 'graph_utils.R'
        'component_analysis.R' 'duplicate_isoforms.R'
        'run_component_ora.R' 'run_fgsea.R' 'gsea_accessors.R'
        'lookup_class.R' 'lookup_vp.R' 'network_diagnostics_class.R'
        'plot_component.R' 'plot_diff_pulldown.R' 'plot_network.R'
        'plot_network_diagnostics.R' 'print_metadata.R'
        'run_differential_pulldown.R' 'run_network_diagnostics.R'
        'transcript_biotypes.R' 'virtual_pulldown.R'
        'virtual_pulldown_analysis.R'
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libglpk-dev
        libicu-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: 2026-11-03 19:51:53 UTC; root
Author: Dimitrios S. Kanakoglou [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7735-2029>),
  Nikolas A. Mumm [aut] (ORCID: <https://orcid.org/0009-0009-5751-0291>),
  Isabella Østerlund [ctb, ths] (Isoform interaction model;
    protein-identical isoform map),
  Kristoffer Vitting-Seerup [cph, ths],
  Isoform Analysis Group [cph]
Maintainer: Dimitrios S. Kanakoglou <dimkan@dtu.dk>