NEWS.md

In GuangchuangYu/DOSE: Disease Ontology Semantic and Enrichment analysis

DOSE 4.0.0

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

DOSE 3.99.1

• return NULL in GSEA if not genes can be mapped (2024-08-26, Mon, ReactomePA#43)

DOSE 3.31.4

• remove mpoSim() and hopSim() (2024-08-21, Wed)

DOSE 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)

DOSE 3.31.2

• add FoldEnrichment, RichFactor and zScore in ORA result (2024-06-13, Thu)

DOSE 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

DOSE 3.30.0

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

DOSE 3.29.2

• fix bugs in get_ont_info() and get_dose_data(): wrong object name and wrong data type (2023-11-30, Thu)

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)
• https://github.com/YuLab-SMU/DOSE/issues/45

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)
• 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

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)
• length > 1 in coercion to logical
• https://github.com/YuLab-SMU/DOSE/pull/32

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)
• 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)

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

• bug fixed of get_enriched (2019-01-14, Mon)
• https://github.com/GuangchuangYu/clusterProfiler/issues/177

DOSE 3.9.2

• mv enrichment vignettes to clusterProfiler-book (2019-01-10, Thu)

DOSE 3.9.1

• asis parameter in [.enrichResult and [.gseaResult (2018-12-24, Mon)
• https://github.com/GuangchuangYu/enrichplot/issues/17

DOSE 3.8

• Bioconductor 3.8 release

DOSE 3.7.1

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

GuangchuangYu/DOSE documentation built on Oct. 31, 2024, 9:15 a.m.