Showing : topgo • reset
1
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 4 weeks ago by ▴ 40 • written 4 weeks ago by • 0
0
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1
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138
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In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 5 weeks ago by 63k • written 5 weeks ago by • 0
0
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0
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111
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
7 weeks ago Priya • 0
1
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1
reply
298
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topGo error loading data
topGO GO
5 months ago peter • 0
1
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0
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296
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
8 months ago Kevin Gregory ▴ 10
0
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4
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780
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How to get significant genes annotated to go term using TopGO?
topGO
updated 10 months ago by ▴ 710 • written 11 months ago by ▴ 10
1
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3
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601
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 11 months ago by 63k • written 11 months ago by ▴ 60
0
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5
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933
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 12 months ago by 63k • written 12 months ago by ▴ 10
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0
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323
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What exactly are Nontrivial node in topGO analysis?
topGO GO
13 months ago theophile • 0
0
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6
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807
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extract significant gene list from specific GO namber
topGO
updated 15 months ago by 63k • written 15 months ago by • 0
4
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7
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1.1k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 15 months ago by ▴ 150 • written 16 months ago by • 0
0
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1
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547
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Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 21 months ago by ▴ 40 • written 21 months ago by • 0
0
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1
reply
460
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 22 months ago by 63k • written 22 months ago by • 0
0
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1
reply
487
views
topGo GenTable returns result column as character
GenTable topGO
updated 2.2 years ago by 63k • written 2.2 years ago by • 0
0
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0
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411
views
topGO weight01 method: potential bug in the code
topGO weight01
2.3 years ago Vladimir • 0
1
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3
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875
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topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 2.3 years ago by ▴ 710 • written 2.3 years ago by • 0
2
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0
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573
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
2.3 years ago Ben ▴ 50
1
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1
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1.0k
views
TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 2.3 years ago by 63k • written 2.3 years ago by • 0
2
votes
1
reply
1.5k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 2.4 years ago by ▴ 20 • written 10.2 years ago by ▴ 340
1
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3
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920
views
topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 2.4 years ago by 63k • written 2.4 years ago by • 0
0
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0
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502
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
2.5 years ago Madza Farias-Virgens • 0
0
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7
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1.5k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 2.6 years ago by 47k • written 2.6 years ago by ▴ 20
0
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4
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782
views
topGO "argument is of length zero" error
GO.db topGO
updated 2.6 years ago by 63k • written 2.6 years ago by • 0
1
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6
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855
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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 2.7 years ago by 63k • written 2.7 years ago by • 0
3
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4
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1.2k
views
Different geneset same p-values in topGO
topgo bug
6.4 years ago • updated 2.7 years ago Lluís Revilla Sancho ▴ 710
4
votes
4
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930
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 2.7 years ago by 47k • written 2.7 years ago by ▴ 120
2
votes
3
replies
665
views
Error in topGO analysis
software error topGO go
updated 2.8 years ago by 3.8k • written 2.8 years ago by • 0
0
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3
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571
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Use topGOdata in devtools package
topGO devtools R
updated 2.8 years ago by 63k • written 2.8 years ago by • 0
1
vote
1
reply
772
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 2.9 years ago by 63k • written 2.9 years ago by ▴ 10
4
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8
replies
4.2k
views
topGO error: allGenes should be a factor or a numeric vector
topGO topgo GO term analysis
updated 2.9 years ago by 3.8k • written 2.9 years ago by ▴ 10
4
votes
8
replies
1.2k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 4 months ago by 63k • written 3.0 years ago by ▴ 30
5
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7
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714
views
Unexpected error with topGO, cannot build topGOdata object
topGO
3.1 years ago abf ▴ 30
0
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1
reply
392
views
Missing ALL library in BiocManager using topGO
topGO
updated 3.1 years ago by 63k • written 3.1 years ago by • 0
1
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3
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1.0k
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TopGO significant genes
TopGO GO
3.1 years ago Al-a ▴ 10
0
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14
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1.4k
views
annFUN error TOPGO
TOPGO annFUN error
updated 3.2 years ago by 3.8k • written 3.2 years ago by • 0
0
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1
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567
views
Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
3.8 years ago s.bourne • 0
3
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3
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751
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 3.9 years ago by 63k • written 3.9 years ago by • 0
2
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2
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1.6k
views
topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 4.0 years ago by 63k • written 4.0 years ago by ▴ 60
0
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3
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943
views
usage of topGO after limma
limma topGO microarray
updated 4.2 years ago by 47k • written 4.2 years ago by • 0
0
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0
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795
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
4.2 years ago psutton • 0
1
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1
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793
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
4.4 years ago David ROUX ▴ 20
0
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1
reply
1.1k
views
topGO: "There are no adj nodes for node"
software error topGO org.hs.eg.db
4.5 years ago natske ▴ 10
2
votes
6
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1.3k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 4.5 years ago by 63k • written 4.5 years ago by • 0
3
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9
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3.9k
views
topGO "invalid argument to unary operator"
software error topgo
updated 4.6 years ago by 63k • written 4.6 years ago by • 0
0
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0
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909
views
topGO analysis runTest: non-numeric argument to binary operator
topGO
4.6 years ago Dave Th. • 0
0
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0
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856
views
topGO: how to print GO descriptions only when using showSigOfNodes?
topgo
4.7 years ago anton.kratz ▴ 60
0
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4
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1.4k
views
How do you specify "chip" in printGenes of TopGO for maize data
TopGo printGenes
updated 4.8 years ago by 63k • written 4.8 years ago by • 0
3
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3
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750
views
DEXUSResult as.data.frame doesn't work well if topGO is loaded
dexus topgo
updated 4.8 years ago by 63k • written 4.8 years ago by • 0
0
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0
replies
497
views
TopGOdata Object error
topgo
4.9 years ago s1607338 • 0
1
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1
reply
706
views
topGO enrichment analysis
topgo
4.9 years ago prakashpandey1111 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
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