Showing : Orgdb • reset
0
votes
5
replies
293
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 10 days ago by 65k • written 13 days ago by • 0
2
votes
2
replies
183
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 15 days ago by 65k • written 15 days ago by • 0
2
votes
1
reply
211
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 5 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
1
vote
3
replies
465
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 5 months ago by 65k • written 5 months ago by • 0
2
votes
4
replies
538
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
6 months ago • updated 12 weeks ago mat149 ▴ 70
0
votes
0
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1.6k
views
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
OrgDb
16 months ago hswdl • 0
1
vote
7
replies
1.5k
views
Adding geneID to list of gene locus IDs
cluster OrgDb clusterProfiler
written 17 months ago by • 0
0
votes
4
replies
1.3k
views
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
OrgDb
16 months ago hendrikwenneker • 0
1
vote
9
replies
1.5k
views
Why is OrgDb linked to specific biocversion? / How to analyze old datasets?
BiocVersion OrgDb clusterProfiler
18 months ago MK • 0
0
votes
1
reply
683
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 19 months ago by 3.9k • written 19 months ago by • 0
0
votes
1
reply
1.2k
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb RNASeq
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
0
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7
replies
4.3k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.1 years ago by • 0 • written 2.5 years ago by • 0
1
vote
2
replies
1.4k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
0
votes
0
replies
849
views
Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
3.0 years ago Thomas.H.Hampton • 0
2
votes
3
replies
1.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.3 years ago by 65k • written 3.3 years ago by ▴ 30
0
votes
2
replies
1.3k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 3.8 years ago by 65k • written 3.8 years ago by ★ 2.0k
3
votes
6
replies
2.2k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 21 months ago by 3.9k • written 4.0 years ago by ★ 2.0k
0
votes
34
replies
8.4k
views
Error: installation of package org.Mm.eg.db had non-zero exit status
OrgDb
updated 4.0 years ago by • 0 • written 4.5 years ago by • 0
7
votes
44
replies
5.4k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 4.8 years ago by 3.9k • written 4.9 years ago by • 0
3
votes
6
replies
1.9k
views
How to create a customized OrgDb in order to perform kegga analysis?
limma kegga orgdb
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
0
votes
1
reply
1.4k
views
News: OrgDbs in AnnotationHub
annotationhub orgdb News
6.5 years ago shepherl 3.9k
0
votes
0
replies
1.3k
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
6.5 years ago shepherl 3.9k
0
votes
6
replies
1.6k
views
Why are important organisms missing from AnnotationHub. Example query(hub, "Zea")
orgdb annotationhub
6.7 years ago slbai01 • 0
0
votes
2
replies
2.0k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
6.8 years ago Didi ▴ 10
1
vote
0
replies
1.2k
views
News: complete set of OrgDb packages have been added to AnnotationHub
bioconductor annotationhub orgdb News
6.9 years ago shepherl 3.9k
0
votes
4
replies
1.4k
views
Annotation Hub object no longer present
Orgdb
7.4 years ago anamabrantesc • 0
2
votes
12
replies
2.3k
views
ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
annotation orgdb
8.2 years ago knishida ▴ 20
3
votes
13
replies
2.6k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub organismdb orgdb unsupported organisms
updated 8.3 years ago by ★ 6.8k • written 8.3 years ago by ★ 3.9k
0
votes
5
replies
1.8k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub orgdb
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Error in makeOrgPackageFromNCBI
GO OrgDb annotate GOstats GO OrgDb annotate GOstats
10.9 years ago Chris Whelan ▴ 60
0
votes
6
replies
1.5k
views
Creating an OrganismDbi package with a few transcript annotations
OrgDb OrganismDbi OrgDb OrganismDbi
updated 11.0 years ago by 25k • written 11.0 years ago by ★ 11k
0
votes
1
reply
1.6k
views
problem creating own org.Ss.eg.db
Annotation GO Organism OrgDb Annotation GO Organism OrgDb
updated 12.2 years ago by ★ 3.9k • written 12.2 years ago by ★ 7.2k
32 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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