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organismdb
•
reset
4
votes
14
replies
1.2k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb
AnnotationForge
7 weeks ago • updated 6 weeks ago
Ozan
• 0
0
votes
3
replies
1.2k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 7 months ago by
Guido Hooiveld
★ 4.0k • written 7 months ago by
Aastha Kapoor
• 0
4
votes
6
replies
1.2k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
13 months ago
abhisek001
• 0
1
vote
2
replies
1.2k
views
annotation: how to use "character" for function 'select()'
annotation
organismdb
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
Guido Hooiveld
★ 4.0k
3
votes
13
replies
2.8k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 8.5 years ago by
Valerie Obenchain
★ 6.8k • written 8.5 years ago by
Guido Hooiveld
★ 4.0k
2
votes
2
replies
2.8k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 8.7 years ago by
Robert Castelo
★ 3.3k • written 8.7 years ago by
efoss
▴ 10
4
votes
3
replies
2.6k
views
ggbio error: Objects of type OrganismDb not supported by autoplot
GO
OrganismDb
ggbio
GO
OrganismDb
ggbio
updated 9.6 years ago by
dalloliogm
▴ 50 • written 9.9 years ago by
Georg Otto
▴ 120
1
vote
2
replies
4.0k
views
Error attaching org.Hs.eg.db package
annotationdbi
annotation
organismdb
loadnamespace
9.7 years ago
milorobertsmith
• 0
2
votes
2
replies
1.3k
views
How to remove IEA genes from list of GO terms?
go
annotation
organismdb
updated 9.8 years ago by
James W. MacDonald
66k • written 9.8 years ago by
Guido Hooiveld
★ 4.0k
1
vote
2
replies
2.2k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb
annotationdbi
annotationforge
updated 9.8 years ago by
Marc Carlson
★ 7.2k • written 9.8 years ago by
artur
▴ 80
0
votes
1
reply
1.5k
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 10.6 years ago by
Matthias Lienhard
▴ 240 • written 10.6 years ago by
Hervé Pagès
16k
0
votes
0
replies
2.0k
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
10.6 years ago
Hervé Pagès
16k
0
votes
0
replies
2.1k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO
Cancer
BSgenome
OrganismDb
SNPlocs
TranscriptDb
Biostrings
BSgenome
rtracklayer
MEDIPS
10.6 years ago
Hervé Pagès
16k
13 results • Page
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
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to
maltethodberg
▴ 180
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to
Michael Love
42k
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Leonardo Collado Torres
★ 1.1k
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to
Gordon Smyth
51k
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