Showing : topGo • reset
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TopGO question
topGO top
updated 6 months ago by 68k • written 6 months ago by • 0
0
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5
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1.2k
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Error when running topGO with KS statistic and elim agorithm
topGO
20 months ago • updated 19 months ago A. denDekker • 0
1
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2
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1.2k
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Access genes associated with GO terms for a topGO object created with gene2GO
topGO
2.0 years ago Dan • 0
0
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2
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1.5k
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enrichPlot error when plotting topGO results
topGO enrichplot
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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1
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1.0k
views
library(topGO) query
topGO scRNAseq
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by • 0
1
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1
reply
1.1k
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.7 years ago by ▴ 40 • written 2.7 years ago by • 0
0
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1
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1.7k
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In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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0
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884
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
2.8 years ago Priya • 0
1
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1
reply
2.1k
views
topGo error loading data
topGO GO
3.1 years ago peter • 0
1
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0
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1.5k
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
3.3 years ago Kevin Gregory ▴ 10
0
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4
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4.8k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 3.5 years ago by ▴ 760 • written 3.5 years ago by ▴ 30
1
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3
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3.3k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 60
0
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5
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3.7k
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GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 30
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0
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984
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What exactly are Nontrivial node in topGO analysis?
topGO GO
3.8 years ago theophile • 0
0
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6
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2.3k
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extract significant gene list from specific GO namber
topGO
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
4
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7
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3.3k
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Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 3.9 years ago by ▴ 180 • written 3.9 years ago by • 0
0
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1
reply
1.7k
views
Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 4.4 years ago by ▴ 40 • written 4.4 years ago by • 0
0
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1
reply
1.4k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
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1
reply
1.3k
views
topGo GenTable returns result column as character
GenTable topGO
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
0
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0
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966
views
topGO weight01 method: potential bug in the code
topGO weight01
4.9 years ago Vladimir • 0
1
vote
3
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2.2k
views
topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 4.9 years ago by ▴ 760 • written 4.9 years ago by • 0
2
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0
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1.5k
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Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
5.0 years ago Ben ▴ 50
1
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1
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2.7k
views
TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
2
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1
reply
2.6k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 5.0 years ago by ▴ 20 • written 12.9 years ago by ▴ 340
1
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3
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2.0k
views
topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
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0
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1.2k
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
5.1 years ago Madza Farias-Virgens • 0
0
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7
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4.9k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 20
0
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4
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1.8k
views
topGO "argument is of length zero" error
GO.db topGO
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
1
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6
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2.3k
views
How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
R TopGO Geneenrichment
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
3
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4
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2.4k
views
Different geneset same p-values in topGO
topgo bug
9.0 years ago • updated 5.3 years ago Lluís Revilla Sancho ▴ 760
4
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4
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2.2k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 120
2
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3
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1.7k
views
Error in topGO analysis
software error topGO go
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
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3
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1.5k
views
Use topGOdata in devtools package
topGO devtools R
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
1
vote
1
reply
1.6k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
4
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8
replies
7.8k
views
topGO error: allGenes should be a factor or a numeric vector
topGO topgo GO term analysis
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
4
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8
replies
3.5k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 3.0 years ago by 68k • written 5.6 years ago by ▴ 30
5
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7
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1.7k
views
Unexpected error with topGO, cannot build topGOdata object
topGO
5.7 years ago abf ▴ 30
0
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1
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1.1k
views
Missing ALL library in BiocManager using topGO
topGO
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
1
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3
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2.3k
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TopGO significant genes
TopGO GO
5.7 years ago Al-a ▴ 10
0
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14
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3.6k
views
annFUN error TOPGO
TOPGO annFUN error
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
0
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1
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1.4k
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Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
6.5 years ago s.bourne • 0
3
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3
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1.9k
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
2
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2
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3.0k
views
topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 60
0
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3
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1.8k
views
usage of topGO after limma
limma topGO microarray
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
0
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0
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1.6k
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topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
6.9 years ago psutton • 0
1
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1
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1.6k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
7.0 years ago David ROUX ▴ 20
0
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1
reply
2.1k
views
topGO: "There are no adj nodes for node"
software error topGO org.hs.eg.db
7.1 years ago natske ▴ 10
2
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6
replies
2.8k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
3
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9
replies
6.8k
views
topGO "invalid argument to unary operator"
software error topgo
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
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0
replies
1.6k
views
topGO analysis runTest: non-numeric argument to binary operator
topGO
7.3 years ago Dave Th. • 0
211 results • Page 1 of 5
Recent ...
Replies
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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