NEWS
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
- bug fixed that introduced in previous commit (2025-10-03, Fri)
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
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
mgeneSim and mclusterSim now always return matrix (2018-08-08, Wed)
GOSemSim 2.5.1
- return NA for deprecated IDs (2018-01-09, Fri)