Changes in version 3.29.2
- fix bugs in get_ont_info() and get_dose_data(): wrong object name
and wrong data type (2023-11-30, Thu)
Changes in version 3.29.1
- mv 'MPO.db' and 'HPO.db' from 'Imports' to 'Suggests' and fixed bugs
(2023-11-18, Sat)
Changes in version 3.28.0
- Bioconductor RELEASE_3_18 (2023-10-25, Wed)
Changes in version 3.27.3
- update TERM2NAME() to return term if corresponding name not found.
(2023-10-09, Mon)
Changes in version 3.27.2
- use 'MPO.db' and 'HPO.db' to support phenotype ontology for mouse
and human (2023-06-30, Fri)
Changes in version 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)
Changes in version 3.26.0
- Bioconductor RELEASE_3_17 (2023-05-03, Wed)
Changes in version 3.24.0
- Bioconductor RELEASE_3_16 (2022-11-02, Wed)
Changes in version 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)
Changes in version 3.23.2
- Support GSON object in GSEA_internal() (2022-06-08, Wed)
Changes in version 3.23.1
- Support GSON object in enricher_internal() (2022-06-06, Mon)
Changes in version 3.22.0
- Bioconductor 3.15 release
Changes in version 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)
Changes in version 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
Changes in version 3.20.0
- Bioconductor 3.14 release
Changes in version 3.19.4
- update clusterProfiler citation (2021-09-30, Thu)
- upate error message of enricher_internal (2021-9-3, Fri)
Changes in version 3.19.3
- upate DisGeNET and NCG data (2021-8-16, Mon)
Changes in version 3.19.2
- bug fixed, change 'is.na(path2name)' to 'all(is.na(path2name))'
(2021-06-21, Mon)
Changes in version 3.19.1
- add dr slot to compareClusterResult, enrichRestul and
gseaResult(2021-5-21, Fri)
Changes in version 3.18
- Bioconductor 3.13 release
Changes in version 3.17
- support setting seed for fgsea method if e.g. gseGO(seed = TRUE)
(2020-10-28, Wed)
- https://github.com/YuLab-SMU/DOSE/issues/45
Changes in version 3.16.0
- Bioconductor 3.12 release (2020-10-28, Wed)
Changes in version 3.15.4
- update setReadable and geneInCategory methods for
compareClusterResult object (2020-10-12, Mon)
Changes in version 3.15.3
- allow passing additional parameters to fgsea (2020-10-09, Fri)
- https://github.com/YuLab-SMU/DOSE/pull/40
- add termsim and method slots to compareClusterResult, enrichRestul
and gseaResult
- https://github.com/YuLab-SMU/DOSE/pull/39
Changes in version 3.15.2
- update NCG and DGN data (2020-10-09, Thu)
Changes in version 3.14.0
- Bioconductor 3.11 release
Changes in version 3.13.2
- fixed issue caused by R v4.0.0 (2020-03-12, Thu)
- length > 1 in coercion to logical
- https://github.com/YuLab-SMU/DOSE/pull/32
Changes in version 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)
Changes in version 3.12.0
- Bioconductor 3.10 release
Changes in version 3.11.2
- ignore universe and print a message if users passing accidentally
passing wrong input (2019-10-24, Thu)
- https://github.com/YuLab-SMU/clusterProfiler/issues/217
- gene with minimal ES value (NES < 0) will be reported in
core_enrichment (2019-07-31, Wed)
Changes in version 3.11.1
- build_Anno now compatible with tibble (2019-05-28, Tue)
Changes in version 3.10.0
- Bioconductor 3.9 release
Changes in version 3.9.4
- export parse_ratio (2019-03-29, Tue)
- bug fixed of get_enriched (2019-01-14, Mon)
- https://github.com/GuangchuangYu/clusterProfiler/issues/177
Changes in version 3.9.2
- mv enrichment vignettes to clusterProfiler-book (2019-01-10, Thu)
Changes in version 3.9.1
- asis parameter in [.enrichResult and [.gseaResult (2018-12-24, Mon)
- https://github.com/GuangchuangYu/enrichplot/issues/17
Changes in version 3.8
- Bioconductor 3.8 release
Changes in version 3.7.1
- S3 accessor methods only return enriched terms. (2018-06-20, Wed)