Showing : topGO • reset
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TopGO question
topGO top
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
0
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5
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969
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Error when running topGO with KS statistic and elim agorithm
topGO
15 months ago A. denDekker • 0
1
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2
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1.1k
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Access genes associated with GO terms for a topGO object created with gene2GO
topGO
20 months ago Dan • 0
0
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2
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1.4k
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enrichPlot error when plotting topGO results
topGO enrichplot
updated 23 months ago by 68k • written 23 months ago by • 0
0
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1
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916
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library(topGO) query
topGO scRNAseq
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
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1
reply
1000
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.4 years ago by ▴ 40 • written 2.4 years ago by • 0
0
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1
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1.6k
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In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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810
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
2.4 years ago Priya • 0
1
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1
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2.0k
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topGo error loading data
topGO GO
2.7 years ago peter • 0
1
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0
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1.4k
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
3.0 years ago Kevin Gregory ▴ 10
0
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4
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4.5k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 3.2 years ago by ▴ 760 • written 3.2 years ago by ▴ 30
1
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3
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3.1k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 60
0
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5
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3.5k
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GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 30
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0
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911
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What exactly are Nontrivial node in topGO analysis?
topGO GO
3.4 years ago theophile • 0
0
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6
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2.1k
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extract significant gene list from specific GO namber
topGO
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
4
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7
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3.1k
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Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 3.6 years ago by ▴ 180 • written 3.6 years ago by • 0
0
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1
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1.6k
views
Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 4.0 years ago by ▴ 40 • written 4.0 years ago by • 0
0
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1
reply
1.2k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
0
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1
reply
1.2k
views
topGo GenTable returns result column as character
GenTable topGO
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
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0
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897
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topGO weight01 method: potential bug in the code
topGO weight01
4.6 years ago Vladimir • 0
1
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3
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2.0k
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topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 4.6 years ago by ▴ 760 • written 4.6 years ago by • 0
2
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0
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1.4k
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Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.6 years ago Ben ▴ 50
1
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1
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2.6k
views
TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
2
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1
reply
2.4k
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topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 4.7 years ago by ▴ 20 • written 12.5 years ago by ▴ 340
1
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3
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1.9k
views
topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
0
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0
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1.1k
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
4.8 years ago Madza Farias-Virgens • 0
0
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7
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4.5k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 4.8 years ago by 53k • written 4.8 years ago by ▴ 20
0
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4
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1.6k
views
topGO "argument is of length zero" error
GO.db topGO
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
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6
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2.1k
views
How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
R TopGO Geneenrichment
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
3
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4
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2.3k
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Different geneset same p-values in topGO
topgo bug
8.7 years ago • updated 5.0 years ago Lluís Revilla Sancho ▴ 760
4
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4
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1.9k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 120
2
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3
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1.6k
views
Error in topGO analysis
software error topGO go
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
0
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3
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1.4k
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Use topGOdata in devtools package
topGO devtools R
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
1
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1
reply
1.5k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 10
4
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8
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7.5k
views
topGO error: allGenes should be a factor or a numeric vector
topGO topgo GO term analysis
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 10
4
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8
replies
3.2k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.6 years ago by 68k • written 5.3 years ago by ▴ 30
5
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7
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1.6k
views
Unexpected error with topGO, cannot build topGOdata object
topGO
5.4 years ago • updated 5.3 years ago abf ▴ 30
0
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1
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1.0k
views
Missing ALL library in BiocManager using topGO
topGO
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
1
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3
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2.1k
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TopGO significant genes
TopGO GO
5.4 years ago Al-a ▴ 10
0
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14
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3.4k
views
annFUN error TOPGO
TOPGO annFUN error
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
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1
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1.3k
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Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
6.1 years ago s.bourne • 0
3
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3
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1.7k
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
2
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2
replies
2.8k
views
topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 60
0
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3
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1.7k
views
usage of topGO after limma
limma topGO microarray
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
0
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0
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1.5k
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topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
6.5 years ago psutton • 0
1
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1
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1.5k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
6.6 years ago David ROUX ▴ 20
0
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1
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2.0k
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topGO: "There are no adj nodes for node"
software error topGO org.hs.eg.db
6.8 years ago natske ▴ 10
2
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6
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2.6k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
3
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9
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6.5k
views
topGO "invalid argument to unary operator"
software error topgo
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
0
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0
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1.5k
views
topGO analysis runTest: non-numeric argument to binary operator
topGO
6.9 years ago Dave Th. • 0
211 results • Page 1 of 5
Recent ...
Replies
Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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