Showing : topgo • reset
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TopGO question
topGO top
updated 9 weeks ago by 68k • written 10 weeks ago by • 0
0
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5
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958
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Error when running topGO with KS statistic and elim agorithm
topGO
15 months ago A. denDekker • 0
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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
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2
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1.4k
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enrichPlot error when plotting topGO results
topGO enrichplot
updated 22 months ago by 68k • written 23 months ago by • 0
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1
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909
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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
992
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.3 years ago by ▴ 40 • written 2.3 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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806
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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
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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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1.3k
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
2.9 years ago Kevin Gregory ▴ 10
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4
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4.4k
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How to get significant genes annotated to go term using TopGO?
topGO
updated 3.1 years ago by ▴ 760 • written 3.2 years ago by ▴ 30
1
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3
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3.1k
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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
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5
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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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900
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What exactly are Nontrivial node in topGO analysis?
topGO GO
3.4 years ago theophile • 0
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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
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1
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1.6k
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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
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1.2k
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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
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1
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1.2k
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topGo GenTable returns result column as character
GenTable topGO
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
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0
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893
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topGO weight01 method: potential bug in the code
topGO weight01
4.5 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
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1
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2.6k
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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
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2.4k
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topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 4.6 years ago by ▴ 20 • written 12.5 years ago by ▴ 340
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3
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1.9k
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topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 4.6 years ago by 68k • written 4.6 years ago by • 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
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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 52k • written 4.8 years ago by ▴ 20
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4
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1.6k
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topGO "argument is of length zero" error
GO.db topGO
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
1
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6
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2.1k
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How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
R TopGO Geneenrichment
updated 4.9 years ago by 68k • written 4.9 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
8.6 years ago • updated 5.0 years ago Lluís Revilla Sancho ▴ 760
4
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4
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1.9k
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Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 5.0 years ago by 52k • 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 5.1 years ago by 68k • written 5.1 years ago by ▴ 10
4
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8
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7.5k
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topGO error: allGenes should be a factor or a numeric vector
topGO topgo GO term analysis
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 10
4
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8
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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
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Unexpected error with topGO, cannot build topGOdata object
topGO
5.3 years ago abf ▴ 30
0
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1
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1.0k
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Missing ALL library in BiocManager using topGO
topGO
updated 5.3 years ago by 68k • written 5.3 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
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14
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3.4k
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annFUN error TOPGO
TOPGO annFUN error
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 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
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2.8k
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topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 60
0
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3
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1.7k
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usage of topGO after limma
limma topGO microarray
updated 6.4 years ago by 52k • written 6.4 years ago by • 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
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How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
6.6 years ago David ROUX ▴ 20
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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
6.7 years ago natske ▴ 10
2
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6
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2.6k
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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
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topGO analysis runTest: non-numeric argument to binary operator
topGO
6.9 years ago Dave Th. • 0
211 results • Page 1 of 5
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Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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