NEWS

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IsoNetAnalyzeR 0.99.0

Version prepared for submission to Bioconductor.

Bundled network

• The bundled network now contains the 158,458 predicted interaction edges (interact == 1) and all 58,164 transcripts, instead of all 2,853,266 scored pairs. Every analysis already restricted the network to these edges, so pulldowns, lookups, components, enrichment and diagnostics are unchanged; this was verified against 0.6.5. Pulldowns are about ten times faster and the source package is under Bioconductor's 5 MB limit.
• Counts of all scored edges change accordingly: the session edge count, the eligibility audit fields edges_before/edges_after, and the diagnostics field full_edges now count predicted interaction edges. plot_network(obj, all_edges = TRUE) on a whole session no longer draws non-interacting pairs.
• inst/scripts/reduce_network.R derives the new network from the 0.6.5 file; inst/PROVENANCE.md documents both checksums.

New features

• get_metadata() returns session metadata such as coverage, seed-support and eligibility audits, replacing direct slot access.
• get_pulldown_graph() returns a gene's up- or down-seeded pulldown graph.
• get_network() returns the session network.
• Network plots label nodes with gene symbols. plot_network() and plot_component() gain node_labels = c("symbol", "id", "none") to switch to transcript or gene identifiers or to hide labels, and gene plot titles show the symbol next to the gene ID. Gene labels in the cross-gene scatter and boxplots also use symbols.
• isonet_gene_names() returns the GENCODE v41 gene symbols of the bundled network (inst/extdata/gene_names_gencode_v41.csv.gz, produced by inst/scripts/make_gene_names.R), for annotating result tables.

Printed output

• Printed summaries are aligned in columns.
• Session creation reports counts with thousands separators and states that excluded NMD and NSD transcripts take their edges with them, which explains the two edge counts.
• "Access with" hints use the name of the variable passed as obj, and the enrichment summaries show "user-supplied" instead of NA for gene sets passed through pathways.

Plot fixes

• The direction = "overlay" plot of plot_network() draws down-only edges dashed and shared edges thicker, has a short centred title with the gene symbol, and puts the legends below the plot.
• Plot titles, axis labels and legends use only characters that R's standard PDF device can draw, so plots saved as PDF keep all their text. The cross-gene boxplots label up-minus-down values "difference (nodes)" and similar instead of using the Greek capital delta.
• Plots of a neighbourhood with only two nodes no longer warn "data length [3] is not a sub-multiple or multiple of the number of rows [2]".
• plot_component(colour_by = "direction") draws one legend for colour and one for seed status instead of two legends both titled "Direction"; equidistant neighbours are labelled "Equidistant".
• The plot_cross_gene_overview() subtitle no longer describes the up/down comparison as a change between conditions.
• The gene-connectivity panel of plot_network_diagnostics() leaves room for the count above its tallest bar.

Documentation and data

• New vignette, "Introduction to IsoNetAnalyzeR", analysing isoform switches between obese type 2 diabetic and lean adipose tissue (GEO GSE141432).
• Example data: gse141432_t2d_vs_lean_seeds.csv (137 seeds of 65 genes) and the MSigDB Hallmark gene sets (msigdb_hallmark_ensembl.rds), with generating scripts in inst/scripts/.
• inst/PROVENANCE.md describes how the network was derived from STRING physical interactions and attributes STRING's CC BY 4.0 licence.
• Every exported function and class has runnable examples.
• The help page for run_network_diagnostics() no longer truncates the description of the default sticky-node rule.

Package infrastructure

• biocViews, URL and BugReports added; ORCID iDs, copyright holders and the thesis supervisors listed in Authors@R; licence declared as MIT + file LICENSE with the full text in LICENSE.md.
• Requires R 4.6.0 or later.
• msigdbr moved to Suggests; withr added to Imports to draw the diagnostics plot subsample with a local seed.

IsoNetAnalyzeR 0.6.5

• Add a concise README with direct user-guide links, a self-contained installed instructions file, and a separate network-eligibility explanation with references.
• Keep the complete MIT licence in a single LICENSE file; update R licence metadata and the README link while preserving the copyright notice and terms.
• Consolidate the default NMD/NSD exclusions from 0.5.5 and the optional retained-significant-seed validation from 0.6.0 into the 0.6.5 release. These scientific rules and the pinned reference resources are unchanged from the checked 0.6.0 analysis archive.
• Separate focal-seed role from neighbourhood membership in differential overlay plots (ISO-PLOT-001). Focal seeds now use a reddish-purple fill (#CC79A7) with directional seed shapes; non-seed nodes and edges use green/up, orange/down and blue/both-direction colours. This corrects the plotting behaviour that was not included in the earlier 0.6.0 archive.
• Add an executable retained-support example to the vignette and full workflow, clarify nonsignificant complementary seeds and the exploratory three-column interface, and update installation and validation instructions for 0.6.5.
• Preserve the raw embedded network, protein-identical transcript map and GENCODE v41 biotype table. Existing checksum-pinned study archives and RNA results remain separate from this release.

IsoNetAnalyzeR 0.6.0

• Add a retained-seed support gate to run_differential_pulldown() via seed_padj_col and seed_fdr. After decay filtering, ID resolution and mapping, every retained gene must contain at least one significant retained seed and at least one up and one down seed. Non-significant complementary seeds remain allowed; there is no seed maximum.
• Store gene/row support audits in metadata$analysis_seed_support. An excluded, unmapped or collapsed-away transcript cannot supply significance for the final seed set.
• RNA testing and effect-size selection remain upstream. The GSE141432 v0.6 analysis enables the gate explicitly; three-column exploratory inputs remain compatible when seed_padj_col = NULL.

IsoNetAnalyzeR 0.5.5

• New sessions exclude annotated NMD and NSD transcripts from protein networks by default. Independent include_nmd/include_nsd flags restore either class explicitly.
• Pinned transcript-biotype annotations and exclusion audits distinguish biological eligibility from statistical seed selection and network coverage.
• Custom networks require known transcript biotypes when exclusions are enabled. Existing saved sessions are unchanged; rebuild them to apply the new policy.
• No maximum seed count is imposed by the package; upstream studies should declare effect/significance rules and whether both directions are required.

IsoNetAnalyzeR 0.5.0

Protein-identical isoform support

• Ship a provenance-checked, transcriptome-wide map from 16,630 redundant transcript identifiers to 9,760 protein representatives. The complete map is available through isonet_duplicate_map(); 10,592 mappings are applicable to the embedded network and 6,038 additional mappings remain available for upstream count aggregation.
• Add resolve_duplicate_isoforms() for version normalization and graph-compatible duplicate resolution. Differential pulldown, direct pulldown, and isoform lookup resolve identifiers by default and retain row-level audits. Set resolve_duplicates = FALSE for the exact identifier behaviour used by 0.4.0.
• Detect pseudo-switches created when oppositely directed submitted isoforms resolve to the same protein representative. Differential analysis drops the affected gene before graph expansion; same-direction collisions collapse to one representative.
• Distinguish cleaned submitted counts from resolved-representative counts. Dominance scores now explicitly use the resolved analysis table.

Count aggregation and validation

• Add aggregate_duplicate_counts() for matrices, data frames, and optional single-assay SummarizedExperiment inputs. It preserves nonmapped features, feature order, gene and library totals, and emits a complete arithmetic and mapping audit.
• Expand coverage reports to show both resolution paths and network outcomes, with submitted and unique-representative totals reported separately.
• Add installed-resource, custom-graph, collision, audit-persistence, count arithmetic, overflow, and optional-container regression tests. The embedded R/sysdata.rda network is unchanged.

IsoNetAnalyzeR 0.4.0

Usability and validation

• Add a persistent three-state network coverage summary: unmapped, mapped without a predicted edge, and mapped with a predicted edge, overall and per supplied direction. Mapping below 10% now emits diagnostic warnings.
• Validate non-finite and fractional integer arguments, stored cutoffs, input duplicates and conflicts, transcript-to-gene mappings, and the complete custom-network contract.
• Support networks with no predicted edges and report complete per-gene processing failure clearly while preserving valid unmapped, isolated, and one-direction results.
• Correct partially missing multi-seed lookups.
• Return plot objects visibly without explicit printing, enabling assignment and headless ggsave() without creating Rplots.pdf.

Documentation

• Define the package as analysis-agnostic and keep seed derivation and publication-specific analyses outside the package.
• Replace proxy-direction examples with a caller-prepared synthetic workflow, qualify compositional dIF guidance, and describe results as static predicted seed neighbourhoods.
• Document reproducible enrichment using seeded runs and frozen pathway lists.

IsoNetAnalyzeR 0.3.2

Correctness fixes

• Preserve mapped isolated seed isoforms and genes through cross-gene graph construction, component analysis, component plotting, single-direction plotting, and differential overlay plotting. A mapped seed with no retained interactions is now represented as a valid one-node/zero-edge result.
• Correct gene-level component bookkeeping so ENSG vertices are compared with gene identifiers rather than ENST seed identifiers when counting direction contributions.
• Plot a stored component using its authoritative node-table membership, so component IDs remain correct when component filters were used.
• Store explicit per-node seed flags in virtual-pulldown statistics, retaining a legacy fallback for serialized objects created before version 0.3.2.
• Give singleton summaries finite structural conventions (density, average degree, and clustering equal to zero; centralization remains undefined).

Documentation and maintenance

• Correct package author/maintainer metadata, Rd markup, and tidy-evaluation global-variable declarations.
• Transfer release maintenance to Dimitrios S. Kanakoglou while retaining Nikolas Mumm as the original package author.
• Correct the GitHub installation URL, vignette name, and cross-gene summary column count in the README and vignette.
• Add regression and end-to-end tests covering gene/isoform component counts, isolated seeds, explicit filters, plotting, serialization, invalid public inputs, fully unmapped analyses, typed empty outputs, and single-direction sparse analyses.
• Run plotting regressions on an explicit temporary graphics device so package tests cannot leave Rplots.pdf in the source tree.
• Replace soft-deprecated igraph plotting aliases with their current API names; singleton and filtered plotting now complete without deprecation warnings and retain identical graph semantics.