NEWS
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)
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)
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)
- add
termsim
and method
slots to compareClusterResult
, enrichRestul
and gseaResult
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)
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)
- 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
DOSE 3.9.4
- export
parse_ratio
(2019-03-29, Tue)
- bug fixed of
get_enriched
(2019-01-14, Mon)
DOSE 3.9.2
DOSE 3.9.1
asis
parameter in [.enrichResult
and [.gseaResult
(2018-12-24, Mon)
DOSE 3.8
DOSE 3.7.1
- S3 accessor methods only return enriched terms. (2018-06-20, Wed)