Showing : TOPGO • reset
1
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615
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Access genes associated with GO terms for a topGO object created with gene2GO
topGO
3 months ago Dan • 0
0
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2
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613
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enrichPlot error when plotting topGO results
topGO enrichplot
updated 6 months ago by 65k • written 6 months ago by • 0
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1
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569
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library(topGO) query
topGO scRNAseq
updated 9 months ago by ▴ 780 • written 9 months ago by • 0
1
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1
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564
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 12 months ago by ▴ 40 • written 12 months ago by • 0
0
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1
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785
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In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 12 months ago by 65k • written 12 months ago by • 0
0
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0
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460
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
12 months ago Priya • 0
1
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1
reply
1.1k
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topGo error loading data
topGO GO
16 months ago peter • 0
1
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0
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789
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
19 months ago Kevin Gregory ▴ 10
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4
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2.6k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 22 months ago by ▴ 730 • written 22 months ago by ▴ 10
1
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3
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1.6k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 22 months ago by 65k • written 22 months ago by ▴ 60
0
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5
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2.0k
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GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 23 months ago by 65k • written 23 months ago by ▴ 10
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0
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590
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What exactly are Nontrivial node in topGO analysis?
topGO GO
2.1 years ago theophile • 0
0
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6
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1.4k
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extract significant gene list from specific GO namber
topGO
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
4
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7
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1.9k
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Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 2.2 years ago by ▴ 150 • written 2.2 years ago by • 0
0
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1
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1.1k
views
Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 2.7 years ago by ▴ 40 • written 2.7 years ago by • 0
0
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1
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850
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Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
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1
reply
852
views
topGo GenTable returns result column as character
GenTable topGO
updated 3.2 years ago by 65k • written 3.2 years ago by • 0
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0
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643
views
topGO weight01 method: potential bug in the code
topGO weight01
3.2 years ago Vladimir • 0
1
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3
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1.4k
views
topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 3.2 years ago by ▴ 730 • written 3.3 years ago by • 0
2
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0
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941
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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
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1
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1.7k
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TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
2
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1
reply
1.9k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 3.3 years ago by ▴ 20 • written 11.2 years ago by ▴ 340
1
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3
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1.3k
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topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
0
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0
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759
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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
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7
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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 50k • written 3.5 years ago by ▴ 20
0
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4
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1.1k
views
topGO "argument is of length zero" error
GO.db topGO
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
1
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6
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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 65k • written 3.6 years ago by • 0
3
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4
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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
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4
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1.3k
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Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 3.6 years ago by 50k • written 3.6 years ago by ▴ 120
2
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3
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1.1k
views
Error in topGO analysis
software error topGO go
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by • 0
0
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3
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953
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Use topGOdata in devtools package
topGO devtools R
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
1
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1
reply
1.1k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 3.8 years ago by 65k • written 3.8 years ago by ▴ 10
4
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8
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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 ★ 3.9k • written 3.8 years ago by ▴ 10
4
votes
8
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2.1k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 15 months ago by 65k • written 3.9 years ago by ▴ 30
5
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7
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1.1k
views
Unexpected error with topGO, cannot build topGOdata object
topGO
4.0 years ago abf ▴ 30
0
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1
reply
685
views
Missing ALL library in BiocManager using topGO
topGO
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
1
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3
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1.5k
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TopGO significant genes
TopGO GO
4.0 years ago Al-a ▴ 10
0
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14
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2.2k
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annFUN error TOPGO
TOPGO annFUN error
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
0
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1
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886
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Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
4.8 years ago s.bourne • 0
3
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3
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1.2k
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 4.8 years ago by 65k • written 4.8 years ago by • 0
2
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2
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2.1k
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topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 60
0
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3
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1.3k
views
usage of topGO after limma
limma topGO microarray
updated 5.1 years ago by 50k • written 5.1 years ago by • 0
0
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0
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1.1k
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topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
5.2 years ago psutton • 0
1
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1
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1.1k
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How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
5.3 years ago David ROUX ▴ 20
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1
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1.5k
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topGO: "There are no adj nodes for node"
software error topGO org.hs.eg.db
5.4 years ago natske ▴ 10
2
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6
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1.9k
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topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
3
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9
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4.7k
views
topGO "invalid argument to unary operator"
software error topgo
updated 5.5 years ago by 65k • written 5.5 years ago by • 0
0
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0
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1.1k
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topGO analysis runTest: non-numeric argument to binary operator
topGO
5.6 years ago Dave Th. • 0
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0
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1.2k
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topGO: how to print GO descriptions only when using showSigOfNodes?
topgo
5.7 years ago anton.kratz ▴ 60
0
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4
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1.8k
views
How do you specify "chip" in printGenes of TopGO for maize data
TopGo printGenes
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Votes
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
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