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enrichit 0.2.0

• extend multi-omics integration with pathway-level and topology-level workflows (2026-06-24, Wed)
  • add aggregate_enrichment() for multi-omics Late Fusion at the pathway level by aggregating multiple enrichResult/gseaResult objects
  • support correlation-aware p-value aggregation with method = "brown" in aggregate_omics()
  • support method = "weighted_mean" in aggregate_omics() for signed statistics with layer-specific weights
  • add mnsea() and mnsea_gson() for multi-layer network-based enrichment
  • add prepare_multilayer_network(), propagate_multilayer(), and collapse_multilayer_scores() for the multi-layer propagation pipeline
  • add mnseaResult to store multi-layer diffusion results, collapsed scores, layer weights, and cached explanation tables
  • precompute pathway-level and feature-level explanation caches inside mnseaResult
  • add get_mnsea_contribution() and extract_mnsea_subnetwork() for explanation-ready data extraction
  • provide the generic engine layer for downstream high-level wrappers such as clusterProfiler::mnseGO(), mnseKEGG(), mnseMKEGG(), and mnseWP()
• add aggregate_omics(), harmonize_ids() and select_features_for_ora() to support Multi-omics Early Integration
  • add conflict_policy parameter (“keep_all”, “strict”, “penalty”) to handle directional conflicts in signed statistics (2026-06-23, Tue)
  • support early fusion before ora(), gsea(), and nsea() through a decoupled aggregation layer
  • these workflow helpers, together with aggregate_enrichment(), are designed to be reused by downstream packages for high-level multi-omics analysis
• add get_omics_contribution() and classify_omics_pattern() for Multi-omics contribution tracing
• implement Weighted Enrichment Analysis (2026-06-23, Tue)
  • add weight parameter to ora(), ora_gson(), gsea(), and gsea_gson()
  • support Weighted ORA using Wallenius’ noncentral hypergeometric distribution via the BiasedUrn package
  • support Weighted GSEA by fusing external weights with ranked statistics
• implement Network-based Set Enrichment Analysis (NSEA) (2026-06-23, Tue)
  • add nsea() and nsea_gson() for network-ranked GSEA based on Random Walk with Restart (RWR)
  • add mode = "signed" support in nsea() and nsea_gson() for bidirectional network propagation using signed statistics
  • add prepare_network() for parsing and normalizing edge lists or sparse matrices
  • implement extremely fast RWR using RcppEigen sparse matrix multiplication
  • introduce zero-dependency integration strategy for network propagation followed by multilevel GSEA
  • provide the generic engine layer for downstream high-level wrappers such as clusterProfiler::nseGO(), nseKEGG(), nseMKEGG(), and nseWP()
• align multilevel GSEA rank scaling with fgsea::prepareStats() to reduce result drift relative to the long-used fgsea backend (2026-06-22, Mon)
  • replace the fixed * 1e6 scaling in prepare_gsea_inputs() with fgsea-style total-weight normalization and integer rounding
  • add a regression test that compares gsea(method = "multilevel") against fgsea::fgseaMultilevel() on the same ranked input
• exclude zero-overlap gene sets from ora_gson() before multiple-testing correction (2026-06-22, Mon)
  • keep Count = 0 rows out of p.adjust/qvalue so ORA results match historical DOSE/clusterProfiler behavior
  • resolves inflated adjustment in downstream clusterProfiler::enricher(), enrichKEGG(), and compareCluster() workflows (e.g. compound KEGG analyses, #821 & #819 of ‘clusterProfiler’)

enrichit 0.1.5

• add Bayesian term selection for ORA results (2026-06-16, Tue)
  • add bayes_enrich() for estimating posterior probabilities of active explanatory terms from enrichResult objects
  • add bayes_summary() to return Bayesian enrichment results ordered by posterior probability
  • support candidate term spaces from top ranked result rows, significant as.data.frame() rows, all x@result rows, or explicit term IDs
  • keep the output as an enrichResult object with posterior, posterior odds, Bayesian rank, active flag, and covered-gene columns

enrichit 0.1.4

• fix GSON helper functions (2026-04-06, Mon)
  • correct TERM2NAME() for GSON objects to map gsid to term names properly
  • correct TERMID2EXTID() for GSON objects to return gene vectors by requested term order
  • return character(0) for missing terms to keep downstream behavior stable
  • resolves malformed Description.* columns in downstream clusterProfiler::groupGO()

enrichit 0.1.3

• fix gsea_gson() (2026-03-10, Tue)
  • force sorting of geneList to ensure result object is consistent with input
  • resolves issue with enrichplot::gseaplot showing incorrect metric/color alignment

enrichit 0.1.2

• improve robustness of calculate_qvalue() (2026-02-02, Mon)
  • handle missing qvalue package gracefully
  • retry with different parameters if qvalue() fails
  • handle invalid p-values (NA, infinite, out of range)
• validate p-values in ora_gson() (2026-02-02, Mon)
  • ensure p-values are within [0, 1] range
  • warn and report invalid p-values
• optimize ORA p-value calculation in C++ (2026-02-02, Mon)
  • use phyper instead of summing dhyper for better performance and precision

enrichit 0.1.1

• update setReadable() to support converting gene ID to other types (not limited to SYMBOL) (2026-01-21, Wed)
• add organism slot in compareClusterResult (2026-01-20, Tue)

enrichit 0.1.0

• fix bugs in gsea_gson() and ora_gson() (2026-01-11, Sun)
  • handle missing columns (e.g., qvalues) gracefully by filling with NA
  • handle NA or duplicate gene set IDs in result rownames to prevent errors
• improve robustness of calculate_qvalue() (2026-01-11, Sun)
  • return NA instead of NULL when qvalue calculation fails
• update ora_gson() output columns (2026-01-11, Sun)

enrichit 0.0.9

• add leading edge analysis for GSEA (2026-01-10, Sat)

enrichit 0.0.8

• fixed bugs of multilevel GSEA in p value calculation (2025-12-10, Wed)
  • by learning the source code of ‘fgsea’

enrichit 0.0.7

• add gseaScores function (2025-12-07, Sun)
  • to calculate GSEA scores for a single gene set

enrichit 0.0.6

• add vignette (2025-12-07, Sun)

enrichit 0.0.5

• implement multi-level GSEA algorithm (2025-12-06, Sat)

enrichit 0.0.4

• implement a simplified adaptive early-stopping GSEA algorithm (2025-12-05, Fri)
  • For each gene set:
  • 1. Run initial batch (e.g., 1000 permutations)
  • 2. If p-value > threshold (e.g., 0.05), stop
  • 3. If significant, increase permutations geometrically (2x, 4x, 8x…)
  • 4. Continue until p-value stabilizes or max permutations reached

enrichit 0.0.3

• implement ora_gson and gsea_gson (2025-12-05, Fri)
  • as replacement for enricher_internal and GSEA_internal
• mv helper functions and class definitions from DOSE to enrichit (2025-12-05, Fri)
  • to extend this package as the base package for the clusterProfiler family

enrichplot 0.0.2

• gsea function (2025-12-04, Thu)
  • Gene Set Enrichment Analysis (GSEA) using C++ via Rcpp.

enrichit 0.0.1

• ora function (2025-12-03, Wed)
  • Fast Over-Representation Analysis (ORA) using C++ via Rcpp.

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