Package: IsoNetAnalyzeR 0.99.0

Dimitrios S. Kanakoglou

IsoNetAnalyzeR: Isoform-Level Protein Interaction Network Analysis

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.

Authors:Dimitrios S. Kanakoglou [aut, cre], Nikolas A. Mumm [aut], Isabella Østerlund [ctb, ths], Kristoffer Vitting-Seerup [cph, ths], Isoform Analysis Group [cph]

IsoNetAnalyzeR_0.99.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
IsoNetAnalyzeR/json (API)

# Install 'IsoNetAnalyzeR' in R:

install.packages('IsoNetAnalyzeR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/isoformanalysisgroup/isonetanalyzer/issues

On CRAN:

software network graphandnetwork networkenrichment genesetenrichment alternativesplicing differentialsplicing transcriptomics systemsbiology visualization

3.88 score 5 scripts 44 exports 69 dependencies

Last updated from:7197e6ff5d. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	167
linux-devel	OK	313
source / vignettes	OK	351
linux-release	OK	350
macos-release	OK	216
macos-oldrel	OK	288
windows-devel	OK	308
windows-release	OK	226
windows-oldrel	OK	296
wasm-release	OK	152

Exports:aggregate_duplicate_counts analyze_subgraph get_analysis get_component get_component_ora_result get_component_overview get_cross_gene_summary get_gene_result get_gsea_result get_gsea_stats get_gsea_table get_isoform_stats get_lookup get_lookup_stats get_lookup_subgraph get_metadata get_network get_network_diagnostics get_ora_table get_pulldown_graph isonet_duplicate_map isonet_gene_names isonet_transcript_biotypes IsoNetAnalyzeR list_analyses list_lookups lookup_virtual_pulldown plot_component plot_cross_gene_boxplot plot_cross_gene_boxplot_overview plot_cross_gene_overview plot_cross_gene_scatter plot_network plot_network_diagnostics print_metadata resolve_duplicate_isoforms run_component_analysis run_component_ora run_differential_pulldown run_fgsea run_network_diagnostics set_metadata summarize_subgraphs virtual_pulldown

Dependencies:base64enc BH BiocParallel cachem cli codetools cowplot cpp11 data.table dplyr farver fastmap fastmatch fgsea formatR futile.logger futile.options future future.apply generics ggforce ggplot2 ggraph ggrepel globals glue graphlayouts gridExtra gtable igraph isoband jsonlite labeling lambda.r lattice lifecycle listenv magrittr MASS Matrix memoise parallelly patchwork pillar pkgconfig polyclip progressr purrr R6 RColorBrewer Rcpp RcppArmadillo rlang S7 scales snow stringi stringr systemfonts tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite withr

Introduction to IsoNetAnalyzeR

Rendered fromIsoNetAnalyzeR.Rmdusingknitr::rmarkdown

Last update: 2026-11-02
Started: 2026-11-01

Help page	Topics
Aggregate counts for protein-identical isoforms	aggregate_duplicate_counts
Per-node analysis of a virtual pulldown subgraph	analyze_subgraph
ComponentAnalysis - connected-component analysis of a differential pulldown	ComponentAnalysis-class show,ComponentAnalysis-method
ComponentOraResult - GO over-representation analysis on connected components	ComponentOraResult-class show,ComponentOraResult-method
DifferentialPulldownAnalysis - full differential pulldown analysis result	DifferentialPulldownAnalysis-class show,DifferentialPulldownAnalysis-method
FgseaResult - GSEA result on a differential pulldown analysis	FgseaResult-class show,FgseaResult-method
GeneDiffPulldown - per-gene differential pulldown result	GeneDiffPulldown-class show,GeneDiffPulldown-method
Retrieve a stored analysis result	get_analysis
Get a merged per-node table for a single connected component	get_component
Retrieve a stored component ORA result	get_component_ora_result get_component_ora_result,IsoNetAnalyzeR-method
Get a merged per-component overview table from a ComponentAnalysis result	get_component_overview
Get the cross-gene summary table from a differential pulldown analysis	get_cross_gene_summary get_cross_gene_summary,IsoNetAnalyzeR-method
Get the per-gene result object from a differential pulldown analysis	get_gene_result get_gene_result,IsoNetAnalyzeR-method
Retrieve a stored GSEA result from a differential pulldown analysis	get_gsea_result get_gsea_result,IsoNetAnalyzeR-method
Get the ranked gene statistic from a GSEA result as a data frame	get_gsea_stats get_gsea_stats,IsoNetAnalyzeR-method
Get the GSEA result table from a differential pulldown analysis	get_gsea_table get_gsea_table,IsoNetAnalyzeR-method
Get combined isoform-level statistics for a gene from a differential pulldown analysis	get_isoform_stats get_isoform_stats,IsoNetAnalyzeR-method
Retrieve a stored lookup result	get_lookup
Get the per-node statistics from a virtual pulldown look-up	get_lookup_stats get_lookup_stats,IsoNetAnalyzeR-method
Get the subgraph from a virtual pulldown look-up	get_lookup_subgraph get_lookup_subgraph,IsoNetAnalyzeR-method
Retrieve metadata from an IsoNetAnalyzeR session object	get_metadata
Retrieve the interaction network of an IsoNetAnalyzeR session	get_network
Retrieve the network diagnostics result from an IsoNetAnalyzeR object	get_network_diagnostics get_network_diagnostics,IsoNetAnalyzeR-method
Get the ORA result table from a component analysis	get_ora_table get_ora_table,IsoNetAnalyzeR-method
Retrieve the up- or down-seeded pulldown graph of one gene	get_pulldown_graph get_pulldown_graph,GeneDiffPulldown-method
Protein-identical isoform identifier map	isonet_duplicate_map
Gene symbols of the bundled network	isonet_gene_names
Transcript biotypes used for protein-network eligibility	isonet_transcript_biotypes
Create a new IsoNetAnalyzeR session object	IsoNetAnalyzeR
IsoNetAnalyzeR - main session object	get_analysis,IsoNetAnalyzeR-method get_lookup,IsoNetAnalyzeR-method IsoNetAnalyzeR-class list_analyses,IsoNetAnalyzeR-method list_lookups,IsoNetAnalyzeR-method show,IsoNetAnalyzeR-method
List stored analysis labels	list_analyses
List stored lookup labels	list_lookups
Perform a virtual pulldown look-up with one or more seeds	lookup_virtual_pulldown
NetworkDiagnostics - network characterisation result	NetworkDiagnostics-class show,NetworkDiagnostics-method
Plot a single connected component from a ComponentAnalysis result	plot_component
Plot cross-gene summary: boxplot of the difference between two columns	plot_cross_gene_boxplot
Overview boxplot: five delta distributions in a single row	plot_cross_gene_boxplot_overview
Overview scatter: six standard up-vs-down comparisons in a 2x3 grid	plot_cross_gene_overview
Plot cross-gene summary: scatter of two columns per gene	plot_cross_gene_scatter
Plot an isoform interaction network	plot_network plot_network,DifferentialPulldownAnalysis-method plot_network,GeneDiffPulldown-method plot_network,IsoNetAnalyzeR-method plot_network,VirtualPulldownLookup-method
Plot network diagnostics	plot_network_diagnostics
Print the metadata of an IsoNetAnalyzeR session object	print_metadata print_metadata,IsoNetAnalyzeR-method
Resolve protein-identical isoform identifiers	resolve_duplicate_isoforms
Run a connected-component analysis on a differential pulldown result	run_component_analysis
Run GO over-representation analysis on connected components	run_component_ora
Run a differential virtual pulldown analysis	run_differential_pulldown
Run GSEA on a differential pulldown analysis	run_fgsea
Run a comprehensive network diagnostics analysis	run_network_diagnostics
Set a metadata field on an IsoNetAnalyzeR session object	set_metadata
Summarize a list of virtual pulldown subgraphs	summarize_subgraphs
Virtual pulldown	virtual_pulldown
VirtualPulldownLookup - single quick virtual pulldown look-up	show,VirtualPulldownLookup-method VirtualPulldownLookup-class

Package: IsoNetAnalyzeR 0.99.0

IsoNetAnalyzeR: Isoform-Level Protein Interaction Network Analysis

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