Showing : TopGO • reset
1
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599
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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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586
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enrichPlot error when plotting topGO results
topGO enrichplot
updated 6 months ago by 65k • written 6 months ago by • 0
0
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1
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549
views
library(topGO) query
topGO scRNAseq
updated 9 months ago by ▴ 780 • written 9 months ago by • 0
1
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1
reply
549
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 11 months ago by ▴ 40 • written 11 months ago by • 0
0
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1
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757
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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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449
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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
4
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8
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2.1k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 14 months ago by 65k • written 3.9 years ago by ▴ 30
1
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1
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1.0k
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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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779
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
19 months ago Kevin Gregory ▴ 10
0
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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 21 months ago by ▴ 730 • written 21 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
0
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0
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579
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What exactly are Nontrivial node in topGO analysis?
topGO GO
2.0 years ago theophile • 0
0
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6
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1.4k
views
extract significant gene list from specific GO namber
topGO
updated 2.1 years ago by 65k • written 2.1 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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1.0k
views
Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 2.6 years ago by ▴ 40 • written 2.7 years ago by • 0
0
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1
reply
836
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Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
0
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1
reply
840
views
topGo GenTable returns result column as character
GenTable topGO
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
0
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0
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637
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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1.3k
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topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 3.2 years ago by ▴ 730 • written 3.2 years ago by • 0
2
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0
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924
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Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3.2 years ago Ben ▴ 50
1
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1
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1.7k
views
TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 3.2 years ago by 65k • written 3.2 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 11.1 years ago by ▴ 340
1
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3
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1.3k
views
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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750
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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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1.4k
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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 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
votes
4
replies
1.3k
views
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 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
0
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3
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944
views
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
replies
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
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
669
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
views
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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874
views
Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
4.7 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
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
5.1 years ago psutton • 0
1
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1
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1.1k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
5.2 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
views
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 5.4 years ago by 65k • written 5.4 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
5.5 years ago Dave Th. • 0
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
5.6 years ago anton.kratz ▴ 60
0
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4
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1.7k
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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Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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