YuLab-SMU DOSE issues - Githubissues

YuLab-SMU / DOSE

:mask: Disease Ontology Semantic and Enrichment analysis

https://yulab-smu.top/biomedical-knowledge-mining-book/

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issues

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`Error in get("DOLite2EG") : object 'DOLite2EG' not found` when re-run `enrichDO`

#85 zxy0912 opened 4 days ago
1
GSEA to discover mixed enriched terms

#84 mauritsunkel opened 3 months ago
1
EXTID2NAME fails to convert geneID to symbol in org.Sc.sgd.db

#83 janedut closed 6 months ago
1
update CITATION

#82 Clearmind777 closed 8 months ago
0
Error in findPathClusters(enrich, cluster = "hier", minClusterSize = 3) : could not find function "findPathClusters"

#81 MANZHAOHUI opened 8 months ago
1
fix bugs in `get_ont_info()` and `get_dose_data()`: wrong object name and wrong data type

#80 huerqiang closed 9 months ago
0
MPO.db/HPO.db installation error

#79 ushione closed 9 months ago
3
MPO.db installation error

#78 eudoraleer opened 10 months ago
6
Fix TERM2NAME() to avoid errors due to mismatch of terms and descriptions

#77 huerqiang closed 11 months ago
0
Seed used in GSEA_fgsea is (almost always) the same

#76 vgilbart opened 1 year ago
0
Support HPO.db and MPO.db

#75 huerqiang closed 1 year ago
0
Parameter "universe" is not properly handled in "enricher" function

#74 soumitrakp closed 11 months ago
3
Query regarding probability computation in enricher_internal function

#73 soumitrakp closed 1 year ago
1
drimseq-error

#72 pragathi-sneha opened 1 year ago
0
use `inherits` to judge the class of objects

#71 huerqiang closed 1 year ago
0
cnetplot for selected gene and GO term

#70 antoine4ucsd closed 1 year ago
1
Error installing latest version of DOSE

#69 archanabhardwaj closed 1 year ago
1
Gson

#68 huerqiang closed 1 year ago
0
update doid-doid data and doid-gene data

#67 huerqiang closed 1 year ago
3
added keyoutput parameter to setReadable and modified EXTID2NAME func…

#66 TriLab-bioinf opened 2 years ago
3
Support passing a GSON object to some functions

#65 huerqiang closed 2 years ago
2
How to add only needed enriched terms in dotplot or cnetplot

#64 pragathi-sneha opened 2 years ago
1
[Feature Request] Allow conversion to columns other than hgnc symbol

#63 Nelson-Gon opened 2 years ago
0
Universal background gene list used in enricher function

#62 merckey opened 2 years ago
1
Enable `setReadable` for compareCluster(GSEA algorithm) result

#61 huerqiang closed 2 years ago
0
change the order of GSEA enrichment result

#60 huerqiang closed 2 years ago
1
Sort decreasing only for DOSE YuLab-SMU/DOSE#58

#59 Nelson-Gon opened 2 years ago
7
Rationale for decreasing order only in GSEA

#58 Nelson-Gon opened 2 years ago
4
DO.db过于老旧

#57 GuangchuangYu opened 2 years ago
2
Update data

#56 huerqiang closed 2 years ago
3
own genelist; too dump top proceed

#55 mocherry opened 2 years ago
3
How does showCategory function work?

#54 smk5g5 closed 2 years ago
2
update error message of `enricher_internal`

#53 huerqiang closed 3 years ago
0
enricher_internal.R code may have mistake

#52 tangmaomao16 opened 3 years ago
1
upate data

#51 huerqiang closed 3 years ago
0
fix a bug

#50 huerqiang closed 3 years ago
0
add `dr` slot to `compareClusterResult`, `enrichRestul` and `gseaResult`

#49 huerqiang closed 3 years ago
0
Saving separate dotplots with for loop

#48 mirkocelii opened 3 years ago
1
No genes mapped by gseNCG

#47 gabrieljmarques closed 3 years ago
0
bug in DOSE:::gseaScores - Error in if (abs(max.ES) > abs(min.ES))

#46 therealgenna opened 3 years ago
9
gseGO through fgsea [ by GSEA_internal() ] is not fully reproducible, but is when running fgsea directly

#45 guidohooiveld closed 3 years ago
2
update setReadable and geneInCategory.compareClusterResult

#44 huerqiang closed 3 years ago
5
setReadable for compareCluster output

#43 GuangchuangYu closed 3 years ago
1
Update setReadable.R

#42 alexyfyf closed 3 years ago
0
setReadable not returning correct gene symbol

#41 alexyfyf closed 2 years ago
4
This fixes a bug where ... aren't passed to fgsea

#40 lgatto closed 3 years ago
3
add termsim and method slots for three class

#39 huerqiang closed 3 years ago
1
Can I make similar ontology package using DOSE？

#38 shangguandong1996 closed 3 years ago
4
Resolves note for non-ASCII characters

#37 huerqiang closed 3 years ago
0
update data

#36 huerqiang closed 3 years ago
2