Showing : OrgDb • reset
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
1
vote
7
replies
1.4k
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
0
votes
4
replies
1.4k
views
Annotation Hub object no longer present
Orgdb
7.4 years ago anamabrantesc • 0
7
votes
44
replies
5.4k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 4.8 years ago by 3.8k • written 4.9 years ago by • 0
3
votes
6
replies
2.2k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 21 months ago by 3.8k • written 3.9 years ago by ★ 2.0k
2
votes
2
replies
144
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 7 days ago by 65k • written 8 days ago by • 0
0
votes
2
replies
2.0k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
6.8 years ago • updated 6.7 years ago Didi ▴ 10
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
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
2
votes
3
replies
1.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 30
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
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
1
vote
3
replies
452
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
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
7
replies
4.3k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.0 years ago by • 0 • written 2.5 years ago by • 0
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
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
2
votes
4
replies
522
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
6 months ago • updated 11 weeks ago mat149 ▴ 70
3
votes
13
replies
2.6k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub organismdb orgdb unsupported organisms
updated 8.2 years ago by ★ 6.8k • written 8.3 years ago by ★ 3.9k
0
votes
5
replies
238
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 2 days ago by 65k • written 5 days ago by • 0
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
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
0
votes
1
reply
1.4k
views
News: OrgDbs in AnnotationHub
annotationhub orgdb News
6.4 years ago shepherl 3.8k
0
votes
1
reply
675
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 18 months ago by 3.8k • written 18 months ago by • 0
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 3.8k
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
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 3.8k
0
votes
0
replies
839
views
Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
3.0 years ago Thomas.H.Hampton • 0
2
votes
1
reply
195
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 4 weeks ago by ★ 3.9k • written 5 weeks ago by ▴ 10
0
votes
0
replies
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
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
32 results • Page 1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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