Showing : topgo • reset
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What exactly are Nontrivial node in topGO analysis?
topGO GO
6 weeks ago theophile • 0
0
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6
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306
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extract significant gene list from specific GO namber
topGO
updated 11 weeks ago by 60k • written 11 weeks ago by • 0
4
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7
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429
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Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 3 months ago by ▴ 140 • written 3 months ago by • 0
0
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1
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228
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Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 9 months ago by ▴ 20 • written 9 months ago by • 0
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1
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222
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Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 9 months ago by 60k • written 9 months ago by • 0
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1
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263
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topGo GenTable returns result column as character
GenTable topGO
updated 14 months ago by 60k • written 14 months ago by • 0
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0
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227
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topGO weight01 method: potential bug in the code
topGO weight01
15 months ago Vladimir • 0
1
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3
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446
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topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 15 months ago by ▴ 660 • written 15 months ago by • 0
2
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0
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289
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Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
16 months ago Ben ▴ 50
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1
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508
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TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 16 months ago by 60k • written 16 months ago by • 0
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1
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1.1k
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topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 16 months ago by • 0 • written 9.2 years ago by ▴ 340
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3
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481
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topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 16 months ago by 60k • written 16 months ago by • 0
0
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0
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293
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
18 months ago Madza Farias-Virgens • 0
0
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7
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798
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 18 months ago by 45k • written 18 months ago by ▴ 20
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4
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525
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topGO "argument is of length zero" error
GO.db topGO
updated 19 months ago by 60k • written 19 months ago by • 0
1
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6
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460
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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 20 months ago by 60k • written 20 months ago by • 0
3
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4
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900
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Different geneset same p-values in topGO
topgo bug
5.4 years ago • updated 20 months ago Lluís Revilla Sancho ▴ 660
4
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4
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579
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Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 20 months ago by 45k • written 20 months ago by ▴ 120
2
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3
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370
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Error in topGO analysis
software error topGO go
updated 21 months ago by 3.5k • written 21 months ago by • 0
0
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3
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335
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Use topGOdata in devtools package
topGO devtools R
updated 21 months ago by 60k • written 21 months ago by • 0
1
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1
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433
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Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 22 months ago by 60k • written 22 months ago by ▴ 10
4
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8
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2.6k
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topGO error: allGenes should be a factor or a numeric vector
topGO topgo GO term analysis
updated 22 months ago by 3.5k • written 22 months ago by ▴ 10
3
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5
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624
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Don't let TopGo to trimm long GO names
go software error topgo rna-seq
2.0 years ago morteza.aslanzadeh ▴ 30
5
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7
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443
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Unexpected error with topGO, cannot build topGOdata object
topGO
2.1 years ago abf ▴ 30
0
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1
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231
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Missing ALL library in BiocManager using topGO
topGO
updated 2.1 years ago by 60k • written 2.1 years ago by • 0
1
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3
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365
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TopGO significant genes
TopGO GO
2.1 years ago Al-a ▴ 10
0
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14
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792
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annFUN error TOPGO
TOPGO annFUN error
updated 2.1 years ago by 3.5k • written 2.1 years ago by • 0
0
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1
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382
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Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
2.8 years ago s.bourne • 0
3
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3
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502
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Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 2.9 years ago by 60k • written 2.9 years ago by • 0
2
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2
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1.1k
views
topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 3.0 years ago by 60k • written 3.0 years ago by ▴ 60
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3
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718
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usage of topGO after limma
limma topGO microarray
updated 3.2 years ago by 45k • written 3.2 years ago by • 0
0
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0
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552
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topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
3.2 years ago psutton • 0
1
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1
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549
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How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
3.3 years ago David ROUX ▴ 10
0
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1
reply
800
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topGO: "There are no adj nodes for node"
software error topGO org.hs.eg.db
3.5 years ago natske ▴ 10
2
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6
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724
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topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 3.5 years ago by 60k • written 3.5 years ago by • 0
3
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9
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2.5k
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topGO "invalid argument to unary operator"
software error topgo
updated 3.5 years ago by 60k • written 3.5 years ago by • 0
0
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0
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745
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topGO analysis runTest: non-numeric argument to binary operator
topGO
3.6 years ago Dave Th. • 0
0
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0
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593
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topGO: how to print GO descriptions only when using showSigOfNodes?
topgo
3.7 years ago anton.kratz ▴ 60
0
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4
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1.1k
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How do you specify "chip" in printGenes of TopGO for maize data
TopGo printGenes
updated 3.8 years ago by 60k • written 3.8 years ago by • 0
3
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3
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564
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DEXUSResult as.data.frame doesn't work well if topGO is loaded
dexus topgo
updated 3.8 years ago by 60k • written 3.8 years ago by • 0
0
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0
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381
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TopGOdata Object error
topgo
3.9 years ago s1607338 • 0
1
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1
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489
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topGO enrichment analysis
topgo
3.9 years ago prakashpandey1111 • 0
2
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4
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699
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topGO: how to rettrieve (long) GO term description without abbreviating
topGO
3.9 years ago al-ash ▴ 50
0
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1
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617
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TopGO ks test using a score different from p-value
topgo ks score kolmogorov-smirnov test go enrichment
updated 3.9 years ago by ▴ 660 • written 3.9 years ago by • 0
1
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0
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1.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
4.2 years ago digrigor ▴ 10
0
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2
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587
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Using topGO for GO Enrichment on methylation markers (Illumina 450k)
topGO illuminahumanmethylation450k.db
4.2 years ago dusan.petrovic • 0
0
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1
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889
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topGO error : could not find function "annotationFun"
topGO R
4.3 years ago User • 0
1
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3
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1.5k
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AffyLib query in topGO
topGO affy
updated 4.3 years ago by 60k • written 4.3 years ago by • 0
0
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1
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557
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Unannotated genes in TopGO
TopGO go analysis
4.3 years ago Yvan Wenger ▴ 50
2
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1
reply
820
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TopGO - Incorrect mapping genes to GO terms
topgo go org.mm.eg.db
updated 4.3 years ago by 60k • written 4.3 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Italicise by Kevin Blighe 3.5k
Okay, I am guessing that the problem is that you need to update the version of *EnhancedVolcano* to the latest version. Can you try that? T…
Comment: Italicise by Pau • 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa by priyanka.m • 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values by wahaha • 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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