Showing : topGO • reset
0
votes
5
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777
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Error when running topGO with KS statistic and elim agorithm
topGO
11 months ago • updated 10 months ago A. denDekker • 0
1
vote
2
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985
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Access genes associated with GO terms for a topGO object created with gene2GO
topGO
15 months ago Dan • 0
0
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2
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1.3k
views
enrichPlot error when plotting topGO results
topGO enrichplot
updated 18 months ago by 68k • written 18 months ago by • 0
0
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1
reply
827
views
library(topGO) query
topGO scRNAseq
updated 21 months ago by ▴ 780 • written 21 months ago by • 0
1
vote
1
reply
888
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 24 months ago by ▴ 40 • written 24 months ago by • 0
0
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1
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1.4k
views
In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
0
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0
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728
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
2.0 years ago Priya • 0
1
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1
reply
1.8k
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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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1.2k
views
adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
2.6 years ago Kevin Gregory ▴ 10
0
votes
4
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4.2k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 2.8 years ago by ▴ 760 • written 2.8 years ago by ▴ 30
1
vote
3
replies
2.9k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 2.8 years ago by 68k • written 2.9 years ago by ▴ 60
0
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5
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3.2k
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 30
0
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0
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808
views
What exactly are Nontrivial node in topGO analysis?
topGO GO
3.0 years ago theophile • 0
0
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6
replies
1.9k
views
extract significant gene list from specific GO namber
topGO
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
4
votes
7
replies
2.8k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 3.2 years ago by ▴ 180 • written 3.2 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
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1
reply
1.2k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
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
833
views
topGO weight01 method: potential bug in the code
topGO weight01
4.2 years ago Vladimir • 0
1
vote
3
replies
1.9k
views
topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 4.2 years ago by ▴ 760 • written 4.2 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
vote
1
reply
2.4k
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 4.3 years ago by ▴ 20 • written 12.1 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 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
0
replies
990
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
4.4 years ago Madza Farias-Virgens • 0
0
votes
7
replies
4.1k
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 4.5 years ago by 68k • written 4.5 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 4.6 years ago by 68k • written 4.6 years ago by • 0
3
votes
4
replies
2.1k
views
Different geneset same p-values in topGO
topgo bug
8.3 years ago • updated 4.6 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 4.6 years ago by 52k • written 4.6 years ago by ▴ 120
2
votes
3
replies
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 4.7 years ago by 68k • written 4.7 years ago by • 0
1
vote
1
reply
1.4k
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
3.0k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.2 years ago by 68k • written 4.9 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
votes
1
reply
918
views
Missing ALL library in BiocManager using topGO
topGO
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
1
vote
3
replies
2.0k
views
TopGO significant genes
TopGO GO
5.0 years ago Al-a ▴ 10
0
votes
14
replies
3.1k
views
annFUN error TOPGO
TOPGO annFUN error
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
0
votes
1
reply
1.2k
views
Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
5.7 years ago s.bourne • 0
3
votes
3
replies
1.6k
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 5.8 years ago by 68k • written 5.8 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 5.9 years ago by 68k • written 5.9 years ago by ▴ 60
0
votes
3
replies
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
replies
1.4k
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
6.1 years ago psutton • 0
1
vote
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
2.4k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
3
votes
9
replies
6.1k
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
1.4k
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
6.6 years ago anton.kratz ▴ 60
50 results • Page 1 of 1
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Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
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[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
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