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OrganismDb
•
reset
4
votes
14
replies
2.6k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb
AnnotationForge
16 months ago
Ozan
• 0
0
votes
3
replies
2.4k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 23 months ago by
Guido Hooiveld
★ 4.1k • written 23 months ago by
Aastha Kapoor
• 0
4
votes
6
replies
1.9k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
2.3 years ago
abhisek001
• 0
1
vote
2
replies
1.6k
views
annotation: how to use "character" for function 'select()'
annotation
organismdb
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
Guido Hooiveld
★ 4.1k
3
votes
13
replies
3.7k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 9.7 years ago by
Valerie Obenchain
★ 6.8k • written 9.8 years ago by
Guido Hooiveld
★ 4.1k
2
votes
2
replies
3.6k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 9.9 years ago by
Robert Castelo
★ 3.4k • written 9.9 years ago by
efoss
▴ 10
4
votes
3
replies
3.0k
views
ggbio error: Objects of type OrganismDb not supported by autoplot
GO
OrganismDb
ggbio
GO
OrganismDb
ggbio
updated 10.9 years ago by
dalloliogm
▴ 50 • written 11.2 years ago by
Georg Otto
▴ 120
1
vote
2
replies
4.4k
views
Error attaching org.Hs.eg.db package
annotationdbi
annotation
organismdb
loadnamespace
11.0 years ago
milorobertsmith
• 0
2
votes
2
replies
1.6k
views
How to remove IEA genes from list of GO terms?
go
annotation
organismdb
updated 11.0 years ago by
James W. MacDonald
68k • written 11.0 years ago by
Guido Hooiveld
★ 4.1k
1
vote
2
replies
2.7k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb
annotationdbi
annotationforge
updated 11.1 years ago by
Marc Carlson
★ 7.2k • written 11.1 years ago by
artur
▴ 80
0
votes
1
reply
5.7k
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 11.9 years ago by
Matthias Lienhard
▴ 280 • written 11.9 years ago by
Hervé Pagès
16k
0
votes
0
replies
2.3k
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
11.9 years ago
Hervé Pagès
16k
0
votes
0
replies
2.4k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO
Cancer
BSgenome
OrganismDb
SNPlocs
TranscriptDb
Biostrings
BSgenome
rtracklayer
MEDIPS
11.9 years ago
Hervé Pagès
16k
13 results • Page
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Comment: Interpretation of output of AffyRNAdeg and hist commands
by
debasainalsa
• 0
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and …
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Votes
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
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