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NEWS.md

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GOSemSim 2.37.2

  • refactor .initial() to use a controlled environment for robust data loading (2026-01-15, Thu)
  • enhance cache reading robustness in computeIC() and wangMethod_internal() (2026-01-15, Thu)
  • update load_onto() documentation (2026-01-12, Mon)
  • enhance godata() input validation (2026-01-12, Mon)
  • refactor internal ontology type checking (2026-01-12, Mon)
  • fix cache integration in .initial and refactor consumers to use get_cache_element (2026-01-12, Mon)
  • fix load_onto() using cache incorrectly (2026-01-12, Mon)
  • use cache mechanisms defined in 'yulab.utils' for caching (2026-01-12, Mon)
  • update URLs, fix typos and refine roxygen documentation (2026-01-12, Mon)

GOSemSim 2.37.1

  • use cache mechanisms defined in 'yulab.utils' for caching (2025-12-08, Mon)
  • update roxygen to use 'markdown' syntax and unify duplicated docs into templates (in 'man-roxygen' folder) (2025-12-07, Sun)
  • move get_organism() from 'DOSE' (2025-12-07, Sun)
  • move load_OrgDb() to 'yulab.utils' (2025-12-05, Fri)

GOSemSim 2.36.0

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

GOSemSim 2.35.2

GOSemSim 2.35.1

  • alternative url for load_onto() (2025-08-12, Tue)

GOSemSim 2.34.0

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

GOSemSim 2.32.0

  • Bioconductor RELEASE_3_20 (2024-10-30, Wed)

GOSemSim 2.31.1

  • get_rel_df() to access ontology relation data frame required by the Wang method (2024-08-13, Tue)
  • a set of 'OntDb' methods for accessing sqlite data generated by the 'obolite' package (2024-08-13, Tue)
  • use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)

GOSemSim 2.30.0

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

GOSemSim 2.29.2

  • update buildGOmap() parameter to be consistent with enricher() and GSEA() (2024-02-06, Tue, #47)

GOSemSim 2.29.1

  • extend godata() to support passing a data.frame (can be output of read.gaf() or read.blast2go()) to 'annoDb' (2023-01-16, Tue)
  • deprecate 'OrgDb' and introduce new parameter 'annoDb' in godata()
  • standardize the output of read.gaf() and read.blast2go()
  • optimize buildGOmap()

GOSemSim 2.28.0

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

GOSemSim 2.27.3

  • use check_installed() to check package dependency (2023-09-12, Tue, #43)

GOSemSim 2.27.2

  • read.blast2go() to parse 'blast2go' result (2023-07-10, Mon, #41, #42)
  • move buildGOmap() and read.gaf() from 'clusterProfiler' (2023-07-10, Mon)

GOSemSim 2.27.1

  • semantic similarity measurement support for MPO (2023-04-06, Thu)
  • TCSS semantic similarity measurement support for DO and MPO (2023-04-06, Thu)

GOSemSim 2.26.0

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

GOSemSim 2.24.0

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

GOSemSim 2.23.1

  • Replacing DO.db with HDO.db (2022-07-29, Mon)

GOSemSim 2.22.0

  • Bioconductor 3.15 release

GOSemSim 2.21.1

  • Avoid eval-parse in load_OrgDb() (2022-01-10, Mon)

GOSemSim 2.20

  • Bioconductor 3.14 release

GOSemSim 2.19.1

  • TCSS method (@qibaiqi, #35; 2021-08-02, Mon)

GOSemSim 2.18.0

  • Bioconductor 3.13 release

GOSemSim 2.17.1

  • bug fixed according to the update of GO.db (2020-10-29, Thu)

GOSemSim 2.16.0

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

GOSemSim 2.15.2

GOSemSim 2.15.1

  • bug fixed of IC method when input IDs contain invalid terms. (2020-07-25, Sat)

GOSemSim 2.14.0

  • Bioconductor 3.11 release

GOSemSim 2.13.1

  • add new citation (2020-03-19, Thu)
  • fixed compiling error due to the change of Rcpp

GOSemSim 2.7.1

GOSemSim 2.5.1