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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 8.4 years ago by
Martin Morgan
25k • written 8.4 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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Comment: WGCNA coupled with differential expression analysis: question about baseline mod
by
hetaf16210
• 0
@[slope][1] If feasible, consider conducting both analyses. Start with a pooled analysis to identify broad patterns, then conduct separate …
Comment: DESeq2 adujsted p-value cutoff seemingly not working
by
980linnet
• 0
Stuck on DESeq2 with alpha=.05 for padj cutoff. Can't seem to get the differential expression analysis to stick the landing - it's like try…
Comment: internal error in trio library when trying to use lfmm() in LEA package
by
PW
• 0
>ERROR: unable to open file D://anole_geno.snmf/K1/run1/anole_geno_r1.1.Q. Please, check that the name of the file you provided is correct.…
Comment: DESeq2 adujsted p-value cutoff seemingly not working
by
Guilherme
• 0
Thank you for your answer So the proper way to conduct the analysis is to put the filters in the results() function and later filter the da…
Comment: DiffBind - observation that the default union overlap is actually a gap of 1 bp
by
Ian D.
▴ 70
Please can you comment on this @rory.
Votes
A: how to extract Granges not overlapping with other ganges?
DESeq2 1.20.0 lfcshrink function
A: LIMMA on RT-PCR data
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
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