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OrganismDb
•
reset
4
votes
14
replies
2.0k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb
AnnotationForge
10 months ago • updated 9 months ago
Ozan
• 0
0
votes
3
replies
2.1k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 16 months ago by
Guido Hooiveld
★ 4.1k • written 16 months ago by
Aastha Kapoor
• 0
4
votes
6
replies
1.6k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
21 months ago
abhisek001
• 0
1
vote
2
replies
1.4k
views
annotation: how to use "character" for function 'select()'
annotation
organismdb
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
Guido Hooiveld
★ 4.1k
3
votes
13
replies
3.3k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 9.2 years ago by
Valerie Obenchain
★ 6.8k • written 9.2 years ago by
Guido Hooiveld
★ 4.1k
2
votes
2
replies
3.3k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 9.4 years ago by
Robert Castelo
★ 3.4k • written 9.4 years ago by
efoss
▴ 10
4
votes
3
replies
2.8k
views
ggbio error: Objects of type OrganismDb not supported by autoplot
GO
OrganismDb
ggbio
GO
OrganismDb
ggbio
updated 10.3 years ago by
dalloliogm
▴ 50 • written 10.6 years ago by
Georg Otto
▴ 120
1
vote
2
replies
4.3k
views
Error attaching org.Hs.eg.db package
annotationdbi
annotation
organismdb
loadnamespace
10.4 years ago
milorobertsmith
• 0
2
votes
2
replies
1.5k
views
How to remove IEA genes from list of GO terms?
go
annotation
organismdb
updated 10.5 years ago by
James W. MacDonald
68k • written 10.5 years ago by
Guido Hooiveld
★ 4.1k
1
vote
2
replies
2.5k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb
annotationdbi
annotationforge
updated 10.5 years ago by
Marc Carlson
★ 7.2k • written 10.5 years ago by
artur
▴ 80
0
votes
1
reply
1.7k
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 11.3 years ago by
Matthias Lienhard
▴ 280 • written 11.3 years ago by
Hervé Pagès
16k
0
votes
0
replies
2.2k
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
11.3 years ago
Hervé Pagès
16k
0
votes
0
replies
2.3k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO
Cancer
BSgenome
OrganismDb
SNPlocs
TranscriptDb
Biostrings
BSgenome
rtracklayer
MEDIPS
11.3 years ago
Hervé Pagès
16k
13 results • Page
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Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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