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OrgDb
•
reset
2
votes
12
replies
2.3k
views
ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
annotation
orgdb
8.3 years ago • updated 8.2 years ago
knishida
▴ 20
1
vote
7
replies
1.5k
views
Adding geneID to list of gene locus IDs
cluster
OrgDb
clusterProfiler
written 17 months ago by
Chruut
• 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
17 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
5.5k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 4.8 years ago by
shepherl
3.9k • written 4.9 years ago by
chirag.parsania
• 0
3
votes
6
replies
2.2k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 22 months ago by
shepherl
3.9k • written 4.0 years ago by
Jenny Drnevich
★ 2.0k
2
votes
2
replies
198
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
sansan
• 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
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
Gordon Smyth
50k • written 6.2 years ago by
baus87
• 0
0
votes
34
replies
8.4k
views
Error: installation of package org.Mm.eg.db had non-zero exit status
OrgDb
updated 4.1 years ago by
Michaël Degaud
• 0 • written 4.6 years ago by
zhangdengwei
• 0
2
votes
3
replies
1.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler
AnnotationDbi
OrgDb
goseq
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
vanbelj
▴ 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
Guido Hooiveld
★ 3.9k • written 3.0 years ago by
ju.ry
• 0
1
vote
3
replies
471
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo
OrgDb
convert
Organismname
RStudio
updated 5 months ago by
James W. MacDonald
65k • written 6 months ago by
j_denton
• 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
Martin Morgan
25k • written 11.0 years ago by
Michael Lawrence
★ 11k
0
votes
7
replies
4.4k
views
how to create an OrgDb package?
orgDb
annotationForge
updated 2.1 years ago by
pengxinyang12
• 0 • written 2.6 years ago by
Haibo Liu
• 0
0
votes
5
replies
1.8k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub
orgdb
updated 8.5 years ago by
Valerie Obenchain
★ 6.8k • written 8.5 years ago by
efoss
▴ 10
0
votes
1
reply
1.2k
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb
RNASeq
updated 2.3 years ago by
James W. MacDonald
65k • written 2.3 years ago by
Jonas
• 0
2
votes
4
replies
547
views
Need help generating BSgenome and orgdb
OrgDb
BSgenome
6 months ago • updated 3 months ago
mat149
▴ 70
3
votes
13
replies
2.7k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 8.3 years ago by
Valerie Obenchain
★ 6.8k • written 8.3 years ago by
Guido Hooiveld
★ 3.9k
0
votes
5
replies
307
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 16 days ago by
James W. MacDonald
65k • written 19 days ago by
Gayatri
• 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
James W. MacDonald
65k • written 3.8 years ago by
Jenny Drnevich
★ 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
Guido Hooiveld
★ 3.9k • written 12.2 years ago by
Marc Carlson
★ 7.2k
0
votes
1
reply
1.4k
views
News:
OrgDbs in AnnotationHub
annotationhub
orgdb
News
6.5 years ago
shepherl
3.9k
0
votes
1
reply
687
views
Share Annotation Packages
OrgDb
AnnotationDbi
updated 19 months ago by
shepherl
3.9k • written 19 months ago by
Imad
• 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
3.9k
0
votes
6
replies
1.6k
views
Why are important organisms missing from AnnotationHub. Example query(hub, "Zea")
orgdb
annotationhub
6.8 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
3.9k
0
votes
0
replies
856
views
Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
3.1 years ago
Thomas.H.Hampton
• 0
2
votes
1
reply
218
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 6 weeks ago by
Guido Hooiveld
★ 3.9k • written 7 weeks ago by
enee
▴ 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
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Replies
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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