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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
8 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 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
Guido Hooiveld
★ 4.1k
3
votes
13
replies
3.2k
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 9.1 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
10.3 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
68k • 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 11.2 years ago by
Matthias Lienhard
▴ 280 • written 11.2 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
11.2 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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Replies
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.6k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Comment: MEDIPS - error using MEDIPS.CpGenrich
by
sg
• 0
I have the same error when I use 22 chrs with the paramenters chr.select: Error in h(simpleError(msg, call)) : error in evaluating the …
Comment: Overcoming confounding in batch effect correction
by
mimi
• 0
https://www.bioconductor.org/packages/release/BiocViews.html#___BiologicalQuestion
Comment: GSVA on RNAseq data
by
Robert Castelo
★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Answer: Store Matrix in DataFrame Cell
by
James W. MacDonald
68k
Put it in a list and put the list in a column.
Votes
Overcoming confounding in batch effect correction
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
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