Showing : topGO • reset
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 8.4 years ago by ★ 3.3k • written 8.4 years ago by ▴ 40
8
votes
16
replies
5.6k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 9.4 years ago by ★ 1.1k • written 9.4 years ago by ▴ 10
5
votes
7
replies
1.1k
views
Unexpected error with topGO, cannot build topGOdata object
topGO
4.0 years ago abf ▴ 30
5
votes
2
replies
1.9k
views
What is Nontrivial node in topGO analysis?
topgo
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 10
5
votes
1
reply
1.3k
views
topGO under-representation table
topGO GO
7.2 years ago beachboarder900 ▴ 40
4
votes
7
replies
1.9k
views
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
4
votes
3
replies
2.2k
views
topGO error "No function to select the significant genes provided!"
topgo
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 40
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
4
votes
8
replies
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
4
votes
3
replies
3.9k
views
topGO: significant genes in GO enriched categories
topGO
updated 9.0 years ago by ▴ 30 • written 9.1 years ago by ▴ 140
4
votes
2
replies
2.6k
views
error with display of significant nodes using topGO
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 14.6 years ago by ▴ 400 • written 14.6 years ago by ▴ 340
4
votes
3
replies
2.8k
views
Select the annotation level during GO enrichment
topgo gostats go
updated 9.6 years ago by 65k • written 9.6 years ago by ▴ 80
4
votes
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
3
votes
3
replies
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
3
votes
4
replies
1.7k
views
Trying to account for gene length in topGO analysis
topgo goseq deseq2
updated 7.8 years ago by ▴ 610 • written 7.8 years ago by • 0
3
votes
3
replies
1.0k
views
DEXUSResult as.data.frame doesn't work well if topGO is loaded
dexus topgo
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
3
votes
0
replies
1.7k
views
Interpret topGO reults
topGO reults
8.8 years ago megerdes ▴ 40
3
votes
2
replies
2.3k
views
How to use TopGO with gene symbols extracted from Illumina probes
topgo
updated 8.6 years ago by 65k • written 8.6 years ago by ▴ 50
3
votes
4
replies
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
3
votes
9
replies
4.7k
views
topGO "invalid argument to unary operator"
software error topgo
updated 5.5 years ago by 65k • written 5.5 years ago by • 0
2
votes
6
replies
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
2
votes
2
replies
2.1k
views
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
2
votes
2
replies
3.6k
views
topGO and font size in the graph plots
topGO topGO
updated 6.3 years ago by ▴ 20 • written 15.6 years ago by ▴ 10
2
votes
1
reply
1.1k
views
TopGO 0 nontrivial nodes
topGO topGO
10.8 years ago Dario Strbenac ★ 1.5k
2
votes
4
replies
2.1k
views
topGO crashes with ' argument "annotationFun" is missing, with no default'
bug topGO
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 160
2
votes
1
reply
2.2k
views
How to get genes corresponding to a GO term from topGOData object?
topGO microarray R gene ontology
updated 6.8 years ago by ▴ 10 • written 8.1 years ago by ▴ 20
2
votes
1
reply
1.2k
views
TopGO - Incorrect mapping genes to GO terms
topgo go org.mm.eg.db
updated 6.2 years ago by 65k • written 6.2 years ago by • 0
2
votes
2
replies
4.3k
views
topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 7.0 years ago by ▴ 730 • written 7.0 years ago by ▴ 10
2
votes
3
replies
1.1k
views
Error in topGO analysis
software error topGO go
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by • 0
2
votes
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
2
votes
0
replies
927
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3.2 years ago Ben ▴ 50
2
votes
4
replies
1.3k
views
topGO: how to rettrieve (long) GO term description without abbreviating
topGO
5.8 years ago al-ash ▴ 50
1
vote
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
1
vote
6
replies
1.4k
views
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
1
vote
1
reply
1.1k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
5.3 years ago David ROUX ▴ 20
1
vote
1
reply
909
views
topGO enrichment analysis
topgo
5.8 years ago prakashpandey1111 • 0
1
vote
0
replies
2.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.1 years ago digrigor ▴ 10
1
vote
3
replies
1.3k
views
topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
1
vote
2
replies
1.4k
views
Error when using the showGroupDensity function in topGO
topGO
updated 7.1 years ago by 65k • written 7.1 years ago by ▴ 30
1
vote
2
replies
2.5k
views
topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 7.3 years ago by ▴ 730 • written 7.6 years ago by ▴ 10
1
vote
1
reply
1.8k
views
Pathview & topGO
R GO topGO pathview
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ▴ 10
1
vote
4
replies
1.6k
views
Obsolete GO terms in topGO analysis
topgo
8.5 years ago s.apocarpum ▴ 10
1
vote
3
replies
1.5k
views
TopGO significant genes
TopGO GO
4.0 years ago Al-a ▴ 10
1
vote
1
reply
1.9k
views
topGO - genesInTerm returns genes not in the annotation
topGO
9.1 years ago samuel collombet ▴ 140
1
vote
1
reply
5.2k
views
Reduce the redundancy of enriched GO terms
GO topgo genesetenrichment
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 150
1
vote
4
replies
4.1k
views
[topGO] More flexible way to select 'interesting' genes
GO probe topGO GO probe topGO
updated 10.7 years ago by ▴ 400 • written 10.7 years ago by ▴ 660
1
vote
0
replies
954
views
New GO terms after TopGO enrichment? (updated)
GO topGO GO topGO
10.5 years ago biotech ▴ 160
1
vote
0
replies
2.1k
views
TopGO p-values VS DAVID p-values
Microarray GO Category topGO Microarray GO Category topGO
12.2 years ago Paul Geeleher ★ 1.3k
1
vote
0
replies
988
views
GO graphs made with topGO are unreadable
GO graph topGO GO graph topGO
11.3 years ago Guest User ★ 13k
1
vote
2
replies
1.2k
views
Absence of GO terms for some genes of interest in topGO package
topgo
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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