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organismdb
•
reset
4
votes
14
replies
1.8k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb
AnnotationForge
7 months ago
Ozan
• 0
0
votes
3
replies
1.9k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 14 months ago by
Guido Hooiveld
★ 4.1k • written 14 months ago by
Aastha Kapoor
• 0
4
votes
6
replies
1.5k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
19 months ago
abhisek001
• 0
1
vote
2
replies
1.4k
views
annotation: how to use "character" for function 'select()'
annotation
organismdb
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
Guido Hooiveld
★ 4.1k
3
votes
13
replies
3.1k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 9.0 years ago by
Valerie Obenchain
★ 6.8k • written 9.0 years ago by
Guido Hooiveld
★ 4.1k
2
votes
2
replies
3.2k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 9.2 years ago by
Robert Castelo
★ 3.4k • written 9.2 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 10.2 years ago by
dalloliogm
▴ 50 • written 10.5 years ago by
Georg Otto
▴ 120
1
vote
2
replies
4.2k
views
Error attaching org.Hs.eg.db package
annotationdbi
annotation
organismdb
loadnamespace
10.2 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 10.3 years ago by
James W. MacDonald
67k • written 10.3 years ago by
Guido Hooiveld
★ 4.1k
1
vote
2
replies
2.4k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb
annotationdbi
annotationforge
updated 10.4 years ago by
Marc Carlson
★ 7.2k • written 10.4 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 11.1 years ago by
Matthias Lienhard
▴ 280 • written 11.1 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
11.1 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
11.2 years ago
Hervé Pagès
16k
13 results • Page
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Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile
by
yf
• 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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