NEWS

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enrichit 0.1.4 (2026-04-08)

• 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 (2026-03-10)

• 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 (2026-02-26)

• 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 (2026-02-01)

• 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 (2026-01-18)

• 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 (2026-01-10)

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

enrichit 0.0.8 (2025-12-22)

• 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

enrichit 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.