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topgo
•
reset
0
votes
0
replies
79
views
What exactly are Nontrivial node in topGO analysis?
topGO
GO
6 weeks ago
theophile
• 0
0
votes
6
replies
306
views
extract significant gene list from specific GO namber
topGO
updated 11 weeks ago by
James W. MacDonald
60k • written 11 weeks ago by
Noy
• 0
4
votes
7
replies
429
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic
org.Sc.sgd.db
pcaExplorer
topGO
EnrichmentBrowser
updated 3 months ago by
Federico Marini
▴ 140 • written 3 months ago by
chase.mateusiak
• 0
0
votes
1
reply
228
views
Help me do a gene enrichment analysis
DESeq2
topGO
heatmaps
updated 9 months ago by
Guandong Shang
▴ 20 • written 9 months ago by
anasjamshed1994
• 0
0
votes
1
reply
222
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 9 months ago by
James W. MacDonald
60k • written 9 months ago by
pedarf
• 0
0
votes
1
reply
263
views
topGo GenTable returns result column as character
GenTable
topGO
updated 14 months ago by
James W. MacDonald
60k • written 14 months ago by
dario.beraldi
• 0
0
votes
0
replies
227
views
topGO weight01 method: potential bug in the code
topGO
weight01
15 months ago
Vladimir
• 0
1
vote
3
replies
446
views
topGO enrichment analysis, ontology selection.
topGO
enrichmentanalysis
geneontology
updated 15 months ago by
Lluís Revilla Sancho
▴ 660 • written 15 months ago by
Aini
• 0
2
votes
0
replies
289
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
16 months ago
Ben
▴ 50
1
vote
1
reply
508
views
TopGO : significant GO term, but 0 gene significant in this GO term (with elim-ks method)
topGO
updated 16 months ago by
James W. MacDonald
60k • written 16 months ago by
Amandine
• 0
0
votes
1
reply
1.1k
views
topGO expected values showing NA
GO
hgu133plus2
topGO
GO
hgu133plus2
topGO
updated 16 months ago by
Doc
• 0 • written 9.2 years ago by
Kishor Tappita
▴ 340
1
vote
3
replies
481
views
topGo custom Annotation table
customannotation
enrichmentanalysis
topGO
updated 16 months ago by
James W. MacDonald
60k • written 16 months ago by
Aini
• 0
0
votes
0
replies
293
views
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
votes
7
replies
798
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange
topGO
DifferentialExpression
enrichment
updated 18 months ago by
Gordon Smyth
45k • written 18 months ago by
lessismore
▴ 20
0
votes
4
replies
525
views
topGO "argument is of length zero" error
GO.db
topGO
updated 19 months ago by
James W. MacDonald
60k • written 19 months ago by
fklirono
• 0
1
vote
6
replies
460
views
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
James W. MacDonald
60k • written 20 months ago by
AP
• 0
3
votes
4
replies
900
views
Different geneset same p-values in topGO
topgo
bug
5.4 years ago • updated 20 months ago
Lluís Revilla Sancho
▴ 660
4
votes
4
replies
579
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO
Gene Ontology
enrichment
panther.db
updated 20 months ago by
Gordon Smyth
45k • written 20 months ago by
Brian Smith
▴ 120
2
votes
3
replies
370
views
Error in topGO analysis
software error
topGO
go
updated 21 months ago by
Kevin Blighe
3.5k • written 21 months ago by
maria.ratto
• 0
0
votes
3
replies
335
views
Use topGOdata in devtools package
topGO
devtools
R
updated 21 months ago by
James W. MacDonald
60k • written 21 months ago by
emisecherre
• 0
1
vote
1
reply
433
views
Error in GO enrichment with topGO
topGO
microarray
Gene ontology
updated 22 months ago by
James W. MacDonald
60k • written 22 months ago by
June.
▴ 10
4
votes
8
replies
2.6k
views
topGO error: allGenes should be a factor or a numeric vector
topGO
topgo
GO term analysis
updated 22 months ago by
Kevin Blighe
3.5k • written 22 months ago by
ccha
▴ 10
3
votes
5
replies
624
views
Don't let TopGo to trimm long GO names
go
software error
topgo
rna-seq
2.0 years ago
morteza.aslanzadeh
▴ 30
5
votes
7
replies
443
views
Unexpected error with topGO, cannot build topGOdata object
topGO
2.1 years ago
abf
▴ 30
0
votes
1
reply
231
views
Missing ALL library in BiocManager using topGO
topGO
updated 2.1 years ago by
James W. MacDonald
60k • written 2.1 years ago by
vladimir.vinarsky
• 0
1
vote
3
replies
365
views
TopGO significant genes
TopGO
GO
2.1 years ago
Al-a
▴ 10
0
votes
14
replies
792
views
annFUN error TOPGO
TOPGO
annFUN
error
updated 2.1 years ago by
Kevin Blighe
3.5k • written 2.1 years ago by
eleonora.porcu
• 0
0
votes
1
reply
382
views
Diagnosing topGo issue - single enriched gene per enriched GO term
topGo
gene enrichment
ontology analysis
2.8 years ago
s.bourne
• 0
3
votes
3
replies
502
views
Discrepancies between topGO output and input
go
topGO
gene
ontology
enrichment
updated 2.9 years ago by
James W. MacDonald
60k • written 2.9 years ago by
t.bergmann
• 0
2
votes
2
replies
1.1k
views
topGO package unable to find library(ALL) and data(ALL)
topGO
software error
updated 3.0 years ago by
James W. MacDonald
60k • written 3.0 years ago by
Raito92
▴ 60
0
votes
3
replies
718
views
usage of topGO after limma
limma
topGO
microarray
updated 3.2 years ago by
Gordon Smyth
45k • written 3.2 years ago by
I.V. Lynn
• 0
0
votes
0
replies
552
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO
AnnotationForge
3.2 years ago
psutton
• 0
1
vote
1
reply
549
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO
significant
enrichment
genes
IDs
3.3 years ago
David ROUX
▴ 10
0
votes
1
reply
800
views
topGO: "There are no adj nodes for node"
software error
topGO
org.hs.eg.db
3.5 years ago
natske
▴ 10
2
votes
6
replies
724
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq
topgo
go enrichment
updated 3.5 years ago by
James W. MacDonald
60k • written 3.5 years ago by
jgg
• 0
3
votes
9
replies
2.5k
views
topGO "invalid argument to unary operator"
software error
topgo
updated 3.5 years ago by
James W. MacDonald
60k • written 3.5 years ago by
fshodan
• 0
0
votes
0
replies
745
views
topGO analysis runTest: non-numeric argument to binary operator
topGO
3.6 years ago
Dave Th.
• 0
0
votes
0
replies
593
views
topGO: how to print GO descriptions only when using showSigOfNodes?
topgo
3.7 years ago
anton.kratz
▴ 60
0
votes
4
replies
1.1k
views
How do you specify "chip" in printGenes of TopGO for maize data
TopGo
printGenes
updated 3.8 years ago by
James W. MacDonald
60k • written 3.8 years ago by
Kaperuza
• 0
3
votes
3
replies
564
views
DEXUSResult as.data.frame doesn't work well if topGO is loaded
dexus
topgo
updated 3.8 years ago by
James W. MacDonald
60k • written 3.8 years ago by
idavydov
• 0
0
votes
0
replies
381
views
TopGOdata Object error
topgo
3.9 years ago
s1607338
• 0
1
vote
1
reply
489
views
topGO enrichment analysis
topgo
3.9 years ago
prakashpandey1111
• 0
2
votes
4
replies
699
views
topGO: how to rettrieve (long) GO term description without abbreviating
topGO
3.9 years ago
al-ash
▴ 50
0
votes
1
reply
617
views
TopGO ks test using a score different from p-value
topgo
ks
score
kolmogorov-smirnov test
go enrichment
updated 3.9 years ago by
Lluís Revilla Sancho
▴ 660 • written 3.9 years ago by
eagomezc
• 0
1
vote
0
replies
1.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo
gene ontology
pathway analysis
rnaseq
DEG
4.2 years ago
digrigor
▴ 10
0
votes
2
replies
587
views
Using topGO for GO Enrichment on methylation markers (Illumina 450k)
topGO
illuminahumanmethylation450k.db
4.2 years ago
dusan.petrovic
• 0
0
votes
1
reply
889
views
topGO error : could not find function "annotationFun"
topGO
R
4.3 years ago
User
• 0
1
vote
3
replies
1.5k
views
AffyLib query in topGO
topGO
affy
updated 4.3 years ago by
James W. MacDonald
60k • written 4.3 years ago by
User
• 0
0
votes
1
reply
557
views
Unannotated genes in TopGO
TopGO
go analysis
4.3 years ago
Yvan Wenger
▴ 50
2
votes
1
reply
820
views
TopGO - Incorrect mapping genes to GO terms
topgo
go
org.mm.eg.db
updated 4.3 years ago by
James W. MacDonald
60k • written 4.3 years ago by
lehallib
• 0
50 results • Page
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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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