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TOPGO
•
reset
0
votes
5
replies
253
views
Error when running topGO with KS statistic and elim agorithm
topGO
21 days ago • updated 6 days ago
A. denDekker
• 0
1
vote
2
replies
651
views
Access genes associated with GO terms for a topGO object created with gene2GO
topGO
5 months ago
Dan
• 0
0
votes
2
replies
676
views
enrichPlot error when plotting topGO results
topGO
enrichplot
updated 8 months ago by
James W. MacDonald
66k • written 8 months ago by
nromerov
• 0
0
votes
1
reply
603
views
library(topGO) query
topGO
scRNAseq
updated 10 months ago by
Basti
▴ 780 • written 10 months ago by
Francesco
• 0
1
vote
1
reply
596
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 13 months ago by
belinda.phipson
▴ 40 • written 13 months ago by
Grace
• 0
0
votes
1
reply
848
views
In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 13 months ago by
James W. MacDonald
66k • written 13 months ago by
NEELAM
• 0
0
votes
0
replies
487
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
14 months ago
Priya
• 0
1
vote
1
reply
1.1k
views
topGo error loading data
topGO
GO
17 months ago
peter
• 0
1
vote
0
replies
822
views
adjusted p-values with topGO elim.KS method
topGO
Ontology
DifferentialExpression
20 months ago
Kevin Gregory
▴ 10
0
votes
4
replies
2.8k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 23 months ago by
Lluís Revilla Sancho
▴ 730 • written 23 months ago by
Lucía
▴ 10
1
vote
3
replies
1.8k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation
GeneOntology
topGO
GO
updated 23 months ago by
James W. MacDonald
66k • written 24 months ago by
Raito92
▴ 60
0
votes
5
replies
2.1k
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler
goseq
topGO
DESeq2
updated 2.0 years ago by
James W. MacDonald
66k • written 2.0 years ago by
Lucía
▴ 10
0
votes
0
replies
616
views
What exactly are Nontrivial node in topGO analysis?
topGO
GO
2.2 years ago
theophile
• 0
0
votes
6
replies
1.5k
views
extract significant gene list from specific GO namber
topGO
updated 2.3 years ago by
James W. MacDonald
66k • written 2.3 years ago by
Noy
• 0
4
votes
7
replies
2.0k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic
org.Sc.sgd.db
pcaExplorer
topGO
EnrichmentBrowser
updated 2.3 years ago by
Federico Marini
▴ 150 • written 2.3 years ago by
chase.mateusiak
• 0
0
votes
1
reply
1.1k
views
Help me do a gene enrichment analysis
DESeq2
topGO
heatmaps
updated 2.8 years ago by
Guandong Shang
▴ 40 • written 2.8 years ago by
anasjamshed1994
• 0
0
votes
1
reply
877
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 2.9 years ago by
James W. MacDonald
66k • written 2.9 years ago by
pedarf
• 0
0
votes
1
reply
877
views
topGo GenTable returns result column as character
GenTable
topGO
updated 3.3 years ago by
James W. MacDonald
66k • written 3.3 years ago by
dario.beraldi
• 0
0
votes
0
replies
656
views
topGO weight01 method: potential bug in the code
topGO
weight01
3.3 years ago
Vladimir
• 0
1
vote
3
replies
1.4k
views
topGO enrichment analysis, ontology selection.
topGO
enrichmentanalysis
geneontology
updated 3.4 years ago by
Lluís Revilla Sancho
▴ 730 • written 3.4 years ago by
Aini
• 0
2
votes
0
replies
976
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
3.4 years ago
Ben
▴ 50
1
vote
1
reply
1.7k
views
TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 3.4 years ago by
James W. MacDonald
66k • written 3.4 years ago by
Amandine
• 0
2
votes
1
reply
2.0k
views
topGO expected values showing NA
GO
hgu133plus2
topGO
GO
hgu133plus2
topGO
updated 3.4 years ago by
Doc
▴ 20 • written 11.3 years ago by
Kishor Tappita
▴ 340
1
vote
3
replies
1.4k
views
topGo custom Annotation table
customannotation
enrichmentanalysis
topGO
updated 3.4 years ago by
James W. MacDonald
66k • written 3.4 years ago by
Aini
• 0
0
votes
0
replies
784
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE
hypeR
goTools
GOstats
topGO
3.5 years ago
Madza Farias-Virgens
• 0
0
votes
7
replies
2.4k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange
topGO
DifferentialExpression
enrichment
updated 3.6 years ago by
Gordon Smyth
51k • written 3.6 years ago by
lessismore
▴ 20
0
votes
4
replies
1.2k
views
topGO "argument is of length zero" error
GO.db
topGO
updated 3.6 years ago by
James W. MacDonald
66k • written 3.6 years ago by
fklirono
• 0
1
vote
6
replies
1.5k
views
How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
R
TopGO
Geneenrichment
updated 3.7 years ago by
James W. MacDonald
66k • written 3.7 years ago by
AP
• 0
3
votes
4
replies
1.7k
views
Different geneset same p-values in topGO
topgo
bug
7.4 years ago • updated 3.7 years ago
Lluís Revilla Sancho
▴ 730
4
votes
4
replies
1.3k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO
Gene Ontology
enrichment
panther.db
updated 3.7 years ago by
Gordon Smyth
51k • written 3.7 years ago by
Brian Smith
▴ 120
2
votes
3
replies
1.2k
views
Error in topGO analysis
software error
topGO
go
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
maria.ratto
• 0
0
votes
3
replies
980
views
Use topGOdata in devtools package
topGO
devtools
R
updated 3.9 years ago by
James W. MacDonald
66k • written 3.9 years ago by
emisecherre
• 0
1
vote
1
reply
1.1k
views
Error in GO enrichment with topGO
topGO
microarray
Gene ontology
updated 3.9 years ago by
James W. MacDonald
66k • written 3.9 years ago by
June.
▴ 10
4
votes
8
replies
6.0k
views
topGO error: allGenes should be a factor or a numeric vector
topGO
topgo
GO term analysis
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
ccha
▴ 10
4
votes
8
replies
2.3k
views
Don't let TopGo to trimm long GO names
go
software error
topgo
rna-seq
updated 16 months ago by
James W. MacDonald
66k • written 4.0 years ago by
morteza.aslanzadeh
▴ 30
5
votes
7
replies
1.2k
views
Unexpected error with topGO, cannot build topGOdata object
topGO
4.1 years ago
abf
▴ 30
0
votes
1
reply
703
views
Missing ALL library in BiocManager using topGO
topGO
updated 4.1 years ago by
James W. MacDonald
66k • written 4.1 years ago by
vladimir.vinarsky
• 0
1
vote
3
replies
1.6k
views
TopGO significant genes
TopGO
GO
4.1 years ago
Al-a
▴ 10
0
votes
14
replies
2.3k
views
annFUN error TOPGO
TOPGO
annFUN
error
updated 4.2 years ago by
Kevin Blighe
★ 3.9k • written 4.2 years ago by
eleonora.porcu
• 0
0
votes
1
reply
905
views
Diagnosing topGo issue - single enriched gene per enriched GO term
topGo
gene enrichment
ontology analysis
4.9 years ago
s.bourne
• 0
3
votes
3
replies
1.3k
views
Discrepancies between topGO output and input
go
topGO
gene
ontology
enrichment
updated 4.9 years ago by
James W. MacDonald
66k • written 4.9 years ago by
t.bergmann
• 0
2
votes
2
replies
2.2k
views
topGO package unable to find library(ALL) and data(ALL)
topGO
software error
updated 5.0 years ago by
James W. MacDonald
66k • written 5.0 years ago by
Raito92
▴ 60
0
votes
3
replies
1.3k
views
usage of topGO after limma
limma
topGO
microarray
updated 5.2 years ago by
Gordon Smyth
51k • written 5.2 years ago by
I.V. Lynn
• 0
0
votes
0
replies
1.1k
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO
AnnotationForge
5.3 years ago
psutton
• 0
1
vote
1
reply
1.1k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO
significant
enrichment
genes
IDs
5.4 years ago
David ROUX
▴ 20
0
votes
1
reply
1.6k
views
topGO: "There are no adj nodes for node"
software error
topGO
org.hs.eg.db
5.5 years ago
natske
▴ 10
2
votes
6
replies
2.0k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq
topgo
go enrichment
updated 5.5 years ago by
James W. MacDonald
66k • written 5.5 years ago by
jgg
• 0
3
votes
9
replies
4.8k
views
topGO "invalid argument to unary operator"
software error
topgo
updated 5.6 years ago by
James W. MacDonald
66k • written 5.6 years ago by
fshodan
• 0
0
votes
0
replies
1.2k
views
topGO analysis runTest: non-numeric argument to binary operator
topGO
5.7 years ago
Dave Th.
• 0
0
votes
0
replies
1.2k
views
topGO: how to print GO descriptions only when using showSigOfNodes?
topgo
5.8 years ago
anton.kratz
▴ 60
50 results • Page
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Comment: error loading collectTRI regulon
by
silvaesilva.da
• 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate
by
James W. MacDonald
66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Answer: Limma model.matrix design with batch effect and different life stages proportion
by
Masongeorge
• 0
Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.
Comment: error loading collectTRI regulon
by
deeenes
▴ 50
I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…
Answer: GESA with certain gene list returns no result with human genom, but many result
by
James W. MacDonald
66k
Ideally you would use something better than gene symbols for this. I realize that biologists like gene symbols, but they are really terribl…
Votes
Answer: DESeq2 returns results for group with just one replicate
Answer: DESeq2 returns results for group with just one replicate
Comment: error loading collectTRI regulon
A: Scaling option in fastMNN
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
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