Showing : topgo • reset
0
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5
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Error when running topGO with KS statistic and elim agorithm
topGO
12 months ago • updated 11 months ago A. denDekker • 0
1
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2
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1000
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Access genes associated with GO terms for a topGO object created with gene2GO
topGO
16 months ago Dan • 0
0
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2
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1.3k
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enrichPlot error when plotting topGO results
topGO enrichplot
updated 19 months ago by 68k • written 19 months ago by • 0
0
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1
reply
838
views
library(topGO) query
topGO scRNAseq
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
1
vote
1
reply
908
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
0
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1
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1.5k
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In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
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0
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750
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
2.1 years ago Priya • 0
1
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1
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1.9k
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topGo error loading data
topGO GO
2.4 years ago peter • 0
1
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0
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1.3k
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
2.7 years ago Kevin Gregory ▴ 10
0
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4
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4.3k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 30
1
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3
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3.0k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 60
0
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5
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3.3k
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GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 30
0
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0
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821
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What exactly are Nontrivial node in topGO analysis?
topGO GO
3.1 years ago theophile • 0
0
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6
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2.0k
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extract significant gene list from specific GO namber
topGO
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
4
votes
7
replies
2.9k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 3.3 years ago by ▴ 180 • written 3.3 years ago by • 0
0
votes
1
reply
1.5k
views
Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 3.7 years ago by ▴ 40 • written 3.7 years ago by • 0
0
votes
1
reply
1.2k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
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1
reply
1.1k
views
topGo GenTable returns result column as character
GenTable topGO
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
0
replies
841
views
topGO weight01 method: potential bug in the code
topGO weight01
4.3 years ago Vladimir • 0
1
vote
3
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1.9k
views
topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 4.3 years ago by ▴ 760 • written 4.3 years ago by • 0
2
votes
0
replies
1.3k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.3 years ago Ben ▴ 50
1
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1
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2.5k
views
TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
2
votes
1
reply
2.3k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 4.4 years ago by ▴ 20 • written 12.2 years ago by ▴ 340
1
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3
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1.8k
views
topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
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0
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1.0k
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
4.5 years ago Madza Farias-Virgens • 0
0
votes
7
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4.3k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 4.5 years ago by 52k • written 4.5 years ago by ▴ 20
0
votes
4
replies
1.5k
views
topGO "argument is of length zero" error
GO.db topGO
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
1
vote
6
replies
2.0k
views
How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
R TopGO Geneenrichment
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
3
votes
4
replies
2.2k
views
Different geneset same p-values in topGO
topgo bug
8.3 years ago • updated 4.7 years ago Lluís Revilla Sancho ▴ 760
4
votes
4
replies
1.8k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 4.7 years ago by 52k • written 4.7 years ago by ▴ 120
2
votes
3
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1.5k
views
Error in topGO analysis
software error topGO go
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
0
votes
3
replies
1.3k
views
Use topGOdata in devtools package
topGO devtools R
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
1
vote
1
reply
1.5k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 10
4
votes
8
replies
7.2k
views
topGO error: allGenes should be a factor or a numeric vector
topGO topgo GO term analysis
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 10
4
votes
8
replies
3.1k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.3 years ago by 68k • written 5.0 years ago by ▴ 30
5
votes
7
replies
1.5k
views
Unexpected error with topGO, cannot build topGOdata object
topGO
5.0 years ago abf ▴ 30
0
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1
reply
936
views
Missing ALL library in BiocManager using topGO
topGO
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
1
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3
replies
2.0k
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TopGO significant genes
TopGO GO
5.1 years ago Al-a ▴ 10
0
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14
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3.2k
views
annFUN error TOPGO
TOPGO annFUN error
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
0
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1
reply
1.2k
views
Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
5.8 years ago s.bourne • 0
3
votes
3
replies
1.6k
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
2
votes
2
replies
2.7k
views
topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 60
0
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3
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1.6k
views
usage of topGO after limma
limma topGO microarray
updated 6.1 years ago by 52k • written 6.1 years ago by • 0
0
votes
0
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1.4k
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
6.2 years ago psutton • 0
1
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1
reply
1.4k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
6.3 years ago David ROUX ▴ 20
0
votes
1
reply
1.9k
views
topGO: "There are no adj nodes for node"
software error topGO org.hs.eg.db
6.4 years ago natske ▴ 10
2
votes
6
replies
2.5k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
3
votes
9
replies
6.2k
views
topGO "invalid argument to unary operator"
software error topgo
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
0
replies
1.5k
views
topGO analysis runTest: non-numeric argument to binary operator
topGO
6.6 years ago Dave Th. • 0
0
votes
0
replies
1.6k
views
topGO: how to print GO descriptions only when using showSigOfNodes?
topgo
6.7 years ago anton.kratz ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
It worked, I think I finally understand and accept that fact. Sorry and thank you again !
Comment: parameters of filterByExpr by Gordon Smyth 52k
You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…
Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k
modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…
Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …
Votes
Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
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