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Rank
Views
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Showing :
TopGO
•
reset
1
vote
2
replies
609
views
Access genes associated with GO terms for a topGO object created with gene2GO
topGO
3 months ago
Dan
• 0
0
votes
2
replies
611
views
enrichPlot error when plotting topGO results
topGO
enrichplot
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
nromerov
• 0
0
votes
1
reply
565
views
library(topGO) query
topGO
scRNAseq
updated 9 months ago by
Basti
▴ 780 • written 9 months ago by
Francesco
• 0
1
vote
1
reply
562
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 12 months ago by
belinda.phipson
▴ 40 • written 12 months ago by
Grace
• 0
0
votes
1
reply
780
views
In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
NEELAM
• 0
0
votes
0
replies
458
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
12 months ago
Priya
• 0
4
votes
8
replies
2.1k
views
Don't let TopGo to trimm long GO names
go
software error
topgo
rna-seq
updated 15 months ago by
James W. MacDonald
65k • written 3.9 years ago by
morteza.aslanzadeh
▴ 30
1
vote
1
reply
1.1k
views
topGo error loading data
topGO
GO
16 months ago
peter
• 0
1
vote
0
replies
788
views
adjusted p-values with topGO elim.KS method
topGO
Ontology
DifferentialExpression
19 months ago
Kevin Gregory
▴ 10
0
votes
4
replies
2.6k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 22 months ago by
Lluís Revilla Sancho
▴ 730 • written 22 months ago by
Lucía
▴ 10
1
vote
3
replies
1.6k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation
GeneOntology
topGO
GO
updated 22 months ago by
James W. MacDonald
65k • written 22 months ago by
Raito92
▴ 60
0
votes
5
replies
2.0k
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler
goseq
topGO
DESeq2
updated 23 months ago by
James W. MacDonald
65k • written 23 months ago by
Lucía
▴ 10
0
votes
0
replies
587
views
What exactly are Nontrivial node in topGO analysis?
topGO
GO
2.1 years ago
theophile
• 0
0
votes
6
replies
1.4k
views
extract significant gene list from specific GO namber
topGO
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Noy
• 0
4
votes
7
replies
1.9k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic
org.Sc.sgd.db
pcaExplorer
topGO
EnrichmentBrowser
updated 2.2 years ago by
Federico Marini
▴ 150 • written 2.2 years ago by
chase.mateusiak
• 0
0
votes
1
reply
1.1k
views
Help me do a gene enrichment analysis
DESeq2
topGO
heatmaps
updated 2.7 years ago by
Guandong Shang
▴ 40 • written 2.7 years ago by
anasjamshed1994
• 0
0
votes
1
reply
849
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
pedarf
• 0
0
votes
1
reply
851
views
topGo GenTable returns result column as character
GenTable
topGO
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
dario.beraldi
• 0
0
votes
0
replies
642
views
topGO weight01 method: potential bug in the code
topGO
weight01
3.2 years ago
Vladimir
• 0
1
vote
3
replies
1.4k
views
topGO enrichment analysis, ontology selection.
topGO
enrichmentanalysis
geneontology
updated 3.2 years ago by
Lluís Revilla Sancho
▴ 730 • written 3.2 years ago by
Aini
• 0
2
votes
0
replies
940
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
3.3 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 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
Amandine
• 0
2
votes
1
reply
1.9k
views
topGO expected values showing NA
GO
hgu133plus2
topGO
GO
hgu133plus2
topGO
updated 3.3 years ago by
Doc
▴ 20 • written 11.2 years ago by
Kishor Tappita
▴ 340
1
vote
3
replies
1.3k
views
topGo custom Annotation table
customannotation
enrichmentanalysis
topGO
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
Aini
• 0
0
votes
0
replies
759
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE
hypeR
goTools
GOstats
topGO
3.4 years ago
Madza Farias-Virgens
• 0
0
votes
7
replies
2.3k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange
topGO
DifferentialExpression
enrichment
updated 3.5 years ago by
Gordon Smyth
50k • written 3.5 years ago by
lessismore
▴ 20
0
votes
4
replies
1.1k
views
topGO "argument is of length zero" error
GO.db
topGO
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 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 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
AP
• 0
3
votes
4
replies
1.6k
views
Different geneset same p-values in topGO
topgo
bug
7.3 years ago • updated 3.6 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 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
Brian Smith
▴ 120
2
votes
3
replies
1.1k
views
Error in topGO analysis
software error
topGO
go
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
maria.ratto
• 0
0
votes
3
replies
952
views
Use topGOdata in devtools package
topGO
devtools
R
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
emisecherre
• 0
1
vote
1
reply
1.1k
views
Error in GO enrichment with topGO
topGO
microarray
Gene ontology
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
June.
▴ 10
4
votes
8
replies
5.8k
views
topGO error: allGenes should be a factor or a numeric vector
topGO
topgo
GO term analysis
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
ccha
▴ 10
5
votes
7
replies
1.1k
views
Unexpected error with topGO, cannot build topGOdata object
topGO
4.0 years ago
abf
▴ 30
0
votes
1
reply
682
views
Missing ALL library in BiocManager using topGO
topGO
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
vladimir.vinarsky
• 0
1
vote
3
replies
1.5k
views
TopGO significant genes
TopGO
GO
4.0 years ago
Al-a
▴ 10
0
votes
14
replies
2.2k
views
annFUN error TOPGO
TOPGO
annFUN
error
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
eleonora.porcu
• 0
0
votes
1
reply
886
views
Diagnosing topGo issue - single enriched gene per enriched GO term
topGo
gene enrichment
ontology analysis
4.8 years ago
s.bourne
• 0
3
votes
3
replies
1.2k
views
Discrepancies between topGO output and input
go
topGO
gene
ontology
enrichment
updated 4.8 years ago by
James W. MacDonald
65k • written 4.8 years ago by
t.bergmann
• 0
2
votes
2
replies
2.1k
views
topGO package unable to find library(ALL) and data(ALL)
topGO
software error
updated 4.9 years ago by
James W. MacDonald
65k • written 4.9 years ago by
Raito92
▴ 60
0
votes
3
replies
1.3k
views
usage of topGO after limma
limma
topGO
microarray
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 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
5.2 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
5.3 years ago
David ROUX
▴ 20
0
votes
1
reply
1.5k
views
topGO: "There are no adj nodes for node"
software error
topGO
org.hs.eg.db
5.4 years ago
natske
▴ 10
2
votes
6
replies
1.9k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq
topgo
go enrichment
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
jgg
• 0
3
votes
9
replies
4.7k
views
topGO "invalid argument to unary operator"
software error
topgo
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
fshodan
• 0
0
votes
0
replies
1.1k
views
topGO analysis runTest: non-numeric argument to binary operator
topGO
5.6 years ago
Dave Th.
• 0
0
votes
0
replies
1.2k
views
topGO: how to print GO descriptions only when using showSigOfNodes?
topgo
5.7 years ago
anton.kratz
▴ 60
0
votes
4
replies
1.8k
views
How do you specify "chip" in printGenes of TopGO for maize data
TopGo
printGenes
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
Kaperuza
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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