Changes in version 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)

                       Changes in version 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)

                       Changes in version 1.56.0                        

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

                       Changes in version 1.55.1                        

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

                       Changes in version 1.54.0                        

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

                       Changes in version 1.52.0                        

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

                       Changes in version 1.50.0                        

  - Bioconductor (2024-10-30, Wed)

                       Changes in version 1.49.1                        

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

                       Changes in version 1.48.0                        

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

                       Changes in version 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)

                       Changes in version 1.46.0                        

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

                       Changes in version 1.44.0                        

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

                       Changes in version 1.41.1                        

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

                       Changes in version 1.34.0                        

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