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organismdb
•
reset
4
votes
14
replies
2.1k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb
AnnotationForge
10 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 17 months ago by
Guido Hooiveld
★ 4.1k • written 17 months ago by
Aastha Kapoor
• 0
4
votes
6
replies
1.7k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
22 months ago
abhisek001
• 0
1
vote
2
replies
1.4k
views
annotation: how to use "character" for function 'select()'
annotation
organismdb
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
Guido Hooiveld
★ 4.1k
3
votes
13
replies
3.4k
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 9.3 years ago by
Guido Hooiveld
★ 4.1k
2
votes
2
replies
3.4k
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
2.9k
views
ggbio error: Objects of type OrganismDb not supported by autoplot
GO
OrganismDb
ggbio
GO
OrganismDb
ggbio
updated 10.4 years ago by
dalloliogm
▴ 50 • written 10.7 years ago by
Georg Otto
▴ 120
1
vote
2
replies
4.3k
views
Error attaching org.Hs.eg.db package
annotationdbi
annotation
organismdb
loadnamespace
10.5 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 10.6 years ago by
Marc Carlson
★ 7.2k • written 10.6 years ago by
artur
▴ 80
0
votes
1
reply
2.9k
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 11.4 years ago by
Matthias Lienhard
▴ 280 • written 11.4 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
11.4 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
11.4 years ago
Hervé Pagès
16k
13 results • Page
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Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
donnycrimson
• 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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