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OrganismDb
•
reset
4
votes
14
replies
1.6k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb
AnnotationForge
5 months ago
Ozan
• 0
0
votes
3
replies
1.7k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 11 months ago by
Guido Hooiveld
★ 4.1k • written 11 months ago by
Aastha Kapoor
• 0
4
votes
6
replies
1.4k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
17 months ago
abhisek001
• 0
1
vote
2
replies
1.4k
views
annotation: how to use "character" for function 'select()'
annotation
organismdb
updated 8.2 years ago by
Martin Morgan
25k • written 8.2 years ago by
Guido Hooiveld
★ 4.1k
3
votes
13
replies
3.0k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 8.8 years ago by
Valerie Obenchain
★ 6.8k • written 8.8 years ago by
Guido Hooiveld
★ 4.1k
2
votes
2
replies
3.0k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 9.0 years ago by
Robert Castelo
★ 3.4k • written 9.0 years ago by
efoss
▴ 10
4
votes
3
replies
2.7k
views
ggbio error: Objects of type OrganismDb not supported by autoplot
GO
OrganismDb
ggbio
GO
OrganismDb
ggbio
updated 10.0 years ago by
dalloliogm
▴ 50 • written 10.3 years ago by
Georg Otto
▴ 120
1
vote
2
replies
4.1k
views
Error attaching org.Hs.eg.db package
annotationdbi
annotation
organismdb
loadnamespace
10.0 years ago
milorobertsmith
• 0
2
votes
2
replies
1.4k
views
How to remove IEA genes from list of GO terms?
go
annotation
organismdb
updated 10.1 years ago by
James W. MacDonald
67k • written 10.1 years ago by
Guido Hooiveld
★ 4.1k
1
vote
2
replies
2.3k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb
annotationdbi
annotationforge
updated 10.2 years ago by
Marc Carlson
★ 7.2k • written 10.2 years ago by
artur
▴ 80
0
votes
1
reply
1.6k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation
GO
Cancer
BSgenome
OrganismDb
SNPlocs
TranscriptDb
Biostrings
BSgenome
MEDIPS
updated 10.9 years ago by
Matthias Lienhard
▴ 280 • written 10.9 years ago by
Hervé Pagès
16k
0
votes
0
replies
2.1k
views
Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation
GO
Cancer
BSgenome
OrganismDb
SNPlocs
TranscriptDb
Biostrings
BSgenome
GO
11.0 years ago
Hervé Pagès
16k
0
votes
0
replies
2.2k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO
Cancer
BSgenome
OrganismDb
SNPlocs
TranscriptDb
Biostrings
BSgenome
rtracklayer
MEDIPS
11.0 years ago
Hervé Pagès
16k
13 results • Page
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Replies
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
by
James W. MacDonald
67k
This support site is meant to help people with technical questions about using Bioconductor packages. Your question is probably better suit…
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
Paul
• 0
This is the traceback I got after running AddMotifs if this is informative? ``` 23: stop(wmsg("trying to load regions beyond the boundaries…
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
James W. MacDonald
67k
You will probably have to ask the Signac people. I don't know exactly what is going on under the hood for `AddMotif`, but the `EnsDb` seems…
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
Paul
• 0
Unfortunately I've updated my code with the newest GRCm39 genome, and yet I am still getting the same error.... Is there anything else I ca…
Comment: WGCNA with TPM tables
by
ATpoint
★ 4.5k
WGCNA is not a Bioconductor package, but generally: If you want to do serious analysis then find the raw data. There is no guarantee what …
Votes
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
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