Changes in version 3.99.1 - return NULL in GSEA if not genes can be mapped (2024-08-26, Mon, ReactomePA#43) Changes in version 3.31.4 - remove mpoSim() and hopSim() (2024-08-21, Wed) Changes in version 3.31.3 - remove gseMPO() and gseHPO(), instead using e.g., gseDO(ont="HPO") (2024-08-15, Thu) - remove enrichMPO() and enrichHPO(), instead using e.g., enrichDO(ont="HPO") - unify API and removing the usages of MPO.db and HPO.db - update DO-gene mapping data (2024-08-13, Tue) - remove HDO.db and use new API in GOSemSim (v>=2.31.1) (2024-08-13, Tue) - use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri) Changes in version 3.31.2 - add FoldEnrichment, RichFactor and zScore in ORA result (2024-06-13, Thu) Changes in version 3.31.1 - fixed bug in options(enrichment_force_universe=TRUE) (2024-05-16, Thu) - https://github.com/YuLab-SMU/clusterProfiler/issues/283#issuecomment-2077869230 Changes in version 3.30.0 - Bioconductor RELEASE_3_19 (2024-05-15, Wed) 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)