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DOSE 3.29.1

  • mv 'MPO.db' and 'HPO.db' from 'Imports' to 'Suggests' and fixed bugs (2023-11-18, Sat)

DOSE 3.28.0

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

DOSE 3.27.3

  • update TERM2NAME() to return term if corresponding name not found. (2023-10-09, Mon)

DOSE 3.27.2

  • use 'MPO.db' and 'HPO.db' to support phenotype ontology for mouse and human (2023-06-30, Fri)

DOSE 3.27.1

  • options(enrichment_force_universe = TRUE) will force enrichment analysis to intersect the universe with gene sets (2023-05-03, Wed)
  • use inherits to judge the class of objects (2022-11-20, Sun)
  • test whether slot in GSON object is NULL (e.g., GSON@keytype) when assigning it to enrichment result (2022-11-07, Mon)

DOSE 3.26.0

  • Bioconductor RELEASE_3_17 (2023-05-03, Wed)

DOSE 3.24.0

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

DOSE 3.23.3

  • replace DO.db to HDO.db (2022-10-7, Fri)
  • add values of organism, keytype and setType for GSEA_internal() (2022-09-21, Wed)
  • add values of organism, keytype and ontology for enricher_internal() (2022-09-21, Wed)
  • move inst/extdata/parse-obo.R to HDO.db package (2022-08-29, Mon)
  • rename qvalues to qvalue in gseaResult object (2022-08-29, Mon)

DOSE 3.23.2

  • Support GSON object in GSEA_internal() (2022-06-08, Wed)

DOSE 3.23.1

  • Support GSON object in enricher_internal() (2022-06-06, Mon)

DOSE 3.22.0

  • Bioconductor 3.15 release

DOSE 3.21.2

  • enable setReadable for compareCluster(GSEA algorithm) result(2021-12-13, Mon)
  • update the default order of GSEA result (2021-12-09, Thu)
    • if p.adjust is identical, sorted by abs(NES)

DOSE 3.21.1

  • upate DisGeNET and NCG data (2021-11-14, Sun)
    • DisGeNET v7: 21671 genes, 30170 diseases and 1134942 gene-disease associations
      • 194515 variants, 14155 diseases and 369554 variant-disease associations
    • NCG v7: 3177 cancer genes, 130 diseases and 6095 gene-disease associations

DOSE 3.20.0

  • Bioconductor 3.14 release

DOSE 3.19.4

  • update clusterProfiler citation (2021-09-30, Thu)
  • upate error message of enricher_internal (2021-9-3, Fri)

DOSE 3.19.3

  • upate DisGeNET and NCG data (2021-8-16, Mon)

DOSE 3.19.2

  • bug fixed, change 'is.na(path2name)' to 'all(is.na(path2name))' (2021-06-21, Mon)

DOSE 3.19.1

  • add dr slot to compareClusterResult, enrichRestul and gseaResult(2021-5-21, Fri)

DOSE 3.18

  • Bioconductor 3.13 release

DOSE 3.17

  • support setting seed for fgsea method if e.g. gseGO(seed = TRUE) (2020-10-28, Wed)

DOSE 3.16.0

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

DOSE 3.15.4

  • update setReadable and geneInCategory methods for compareClusterResult object (2020-10-12, Mon)

DOSE 3.15.3

  • allow passing additional parameters to fgsea (2020-10-09, Fri)
  • add termsim and method slots to compareClusterResult, enrichRestul and gseaResult

DOSE 3.15.2

  • update NCG and DGN data (2020-10-09, Thu)

DOSE 3.14.0

  • Bioconductor 3.11 release

DOSE 3.13.2

  • fixed issue caused by R v4.0.0 (2020-03-12, Thu)

DOSE 3.13.1

  • remove S4Vectors dependencies (2019-12-19, Thu)
  • extend setReadable to support compareClusterResult (2019-12-02, Mon)
  • add gene2Symbol, keytype and readable slots for compareClusterResult
  • move compareClusterResult class definition from clusterProfiler (2019-11-01, Fri)

DOSE 3.12.0

  • Bioconductor 3.10 release

DOSE 3.11.2

  • ignore universe and print a message if users passing accidentally passing wrong input (2019-10-24, Thu)
  • gene with minimal ES value (NES < 0) will be reported in core_enrichment (2019-07-31, Wed)

DOSE 3.11.1

  • build_Anno now compatible with tibble (2019-05-28, Tue)

DOSE 3.10.0

  • Bioconductor 3.9 release

DOSE 3.9.4

  • export parse_ratio (2019-03-29, Tue)

DOSE 3.9.4

DOSE 3.9.2

DOSE 3.9.1

DOSE 3.8

  • Bioconductor 3.8 release

DOSE 3.7.1

  • S3 accessor methods only return enriched terms. (2018-06-20, Wed)