NEWS

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ReactomePA 1.99.2

• gsePathway() now exposes eps and forwards extra arguments (...) to enrichit::gsea_gson(), matching the other GSEA wrappers in the family (2026-09-22, Tue, #47)
• gsePathway() and nsePathway() now expose an explicit seed parameter for reproducible GSEA results, aligned with enrichit::gsea_gson(): set it to a number (or TRUE for a fixed default seed) to get identical results across runs; FALSE (default) draws a fresh seed on each run (2026-08-15, Fri)
• prepareReactomeNetwork() is ~40x faster: the per-pathway conversion no longer round-trips through graphite::convertIdentifiers()/pathwayGraph() (whose per-call mapIds() overhead was hash/SQLite-bound and capped parallel scaling at ~4-5 effective cores). It now builds a single UNIPROT->Entrez map up front and converts the protein edges with vectorized lookups, keeping mclapply() parallelization over pathways. The resulting network is identical to the previous output (same nodes and edge values; only node ordering may differ). The default cores is now 1 (serial, ~40 s for human; options(mc.cores=...) or an explicit cores= still enables parallel) instead of detectCores() (2026-08-16, Sat)

ReactomePA 1.99.1

• nsePathway(): network-based set enrichment analysis (NSEA) on the Reactome reaction graph using Random Walk with Restart (2026-07-08, Wed)
• bayes_reactome(): Bayesian term selection for compressing redundant Reactome pathway output via enrichit::bayes_enrich() (2026-07-08, Wed)
• prepareReactomeNetwork(): utility to build and cache the Reactome reaction graph for reuse in nsePathway() (2026-07-08, Wed)
• enrichPathway() and gsePathway() now accept a weight parameter for weighted ORA/GSEA (2026-07-08, Wed)
• migrate caching from custom environment (reactome_env) to yulab.utils::with_cache(); delete get_Reactome_DATA(), getALLEG() (2026-07-08, Wed)
• gson_Reactome() now caches the final GSON object directly, with data cleaning inlined (2026-07-08, Wed)

ReactomePA 1.56.0

• Bioconductor RELEASE_3_23 (2026-04-29, Wed)

ReactomePA 1.55.1

• use 'enrichit' as engine for enrichment analysis (2025-12-07, Sun)

ReactomePA 1.54.0

• Bioconductor RELEASE_3_22 (2025-11-01, Sat)

ReactomePA 1.52.0

• Bioconductor RELEASE_3_21 (2025-04-17, Thu)

ReactomePA 1.50.0

• Bioconductor (2024-10-30, Wed)

ReactomePA 1.49.1

• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)

ReactomePA 1.48.0

• Bioconductor RELEASE_3_19 (2024-05-15, Wed)

ReactomePA 1.47.1

• Add a disclaimer in package Description to claim that this package is not affiliated with the Reactome team (2023-11-17, Fri)

ReactomePA 1.46.0

• Bioconductor RELEASE_3_18 (2023-10-25, Wed)

ReactomePA 1.44.0

• Bioconductor RELEASE_3_16 (2022-11-02, Wed)

ReactomePA 1.41.1

• add function gson_Reactome (2022-7-13, Wed)

ReactomePA 1.34.0

• Bioconductor 3.12 release (2020-10-28, Wed)