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topGO
•
reset
0
votes
0
replies
1.6k
views
topGO: how to print GO descriptions only when using showSigOfNodes?
topgo
7.0 years ago
anton.kratz
▴ 60
0
votes
4
replies
2.2k
views
How do you specify "chip" in printGenes of TopGO for maize data
TopGo
printGenes
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
Kaperuza
• 0
3
votes
3
replies
1.4k
views
DEXUSResult as.data.frame doesn't work well if topGO is loaded
dexus
topgo
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
idavydov
• 0
0
votes
0
replies
890
views
TopGOdata Object error
topgo
7.2 years ago
s1607338
• 0
1
vote
1
reply
1.2k
views
topGO enrichment analysis
topgo
7.2 years ago
prakashpandey1111
• 0
2
votes
4
replies
1.7k
views
topGO: how to rettrieve (long) GO term description without abbreviating
topGO
7.2 years ago
al-ash
▴ 50
0
votes
1
reply
1.6k
views
TopGO ks test using a score different from p-value
topgo
ks
score
kolmogorov-smirnov test
go enrichment
updated 7.2 years ago by
Lluís Revilla Sancho
▴ 760 • written 7.2 years ago by
eagomezc
• 0
1
vote
0
replies
2.7k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo
gene ontology
pathway analysis
rnaseq
DEG
7.5 years ago
digrigor
▴ 10
0
votes
2
replies
1.4k
views
Using topGO for GO Enrichment on methylation markers (Illumina 450k)
topGO
illuminahumanmethylation450k.db
7.5 years ago
dusan.petrovic
• 0
0
votes
1
reply
1.7k
views
topGO error : could not find function "annotationFun"
topGO
R
7.6 years ago
User
• 0
1
vote
3
replies
2.8k
views
AffyLib query in topGO
topGO
affy
updated 7.6 years ago by
James W. MacDonald
68k • written 7.6 years ago by
User
• 0
0
votes
1
reply
1.1k
views
Unannotated genes in TopGO
TopGO
go analysis
7.6 years ago
Yvan Wenger
▴ 50
2
votes
1
reply
1.6k
views
TopGO - Incorrect mapping genes to GO terms
topgo
go
org.mm.eg.db
updated 7.6 years ago by
James W. MacDonald
68k • written 7.6 years ago by
lehallib
• 0
0
votes
4
replies
1.8k
views
Error topGO printGenes
topGo
7.6 years ago
irving.jgalo23
• 0
0
votes
1
reply
1.9k
views
using other ontologies in topGO && building GO.db like database for GO-like ontologies
GO
topGO
GO
topGO
updated 7.7 years ago by
Yvan Wenger
▴ 50 • written 11.5 years ago by
Xin.H
▴ 10
2
votes
2
replies
4.2k
views
topGO and font size in the graph plots
topGO
topGO
updated 7.7 years ago by
shaungarnett
▴ 20 • written 16.9 years ago by
Shankavaram, Uma NIH/NCI [E]
▴ 10
0
votes
6
replies
2.0k
views
ENSEMBL causing issues replicating previous results
R
ENSEMBL
topGO
7.7 years ago
snguyen268
• 0
0
votes
1
reply
1.4k
views
topGO - Extra terms appearing in main analysis and the enrichment test
gene ontology
topGO
GO
7.8 years ago
beachboarder900
▴ 40
0
votes
2
replies
1.9k
views
GO analysis under-represented genes and over-represented (enrichment) down-regulated genes
go
rnaseq
clusterprofiler
topgo
7.9 years ago
Jack
▴ 20
0
votes
0
replies
1.8k
views
How to plot the top_GO result using GOplot?
topgo
Goplot
7.9 years ago
peirinl
• 0
0
votes
0
replies
1.1k
views
Problem in genelist levels when running topGO.
topgo
7.9 years ago
peirinl
• 0
0
votes
8
replies
2.6k
views
How to produce png files from printGraph
topgo
updated 7.9 years ago by
arendsee
▴ 10 • written 7.9 years ago by
mictadlo
▴ 10
0
votes
1
reply
3.4k
views
Error in xy.coords(x, y, xlabel, ylabel, log)
topgo
svg
7.9 years ago
mictadlo
▴ 10
0
votes
3
replies
3.1k
views
topGO - missing value where TRUE/FALSE needed
topgo
edger
8.0 years ago
mictadlo
▴ 10
0
votes
2
replies
1.6k
views
how to build gene.pathway data.frame for non-model organism
limma
kegg
topgo
dataframe
edger
8.0 years ago
mictadlo
▴ 10
0
votes
5
replies
3.3k
views
How to use topGO and KEGG with de-novo species
topgo
edger
limma
kegga
kegg
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
mictadlo
▴ 10
0
votes
0
replies
1.1k
views
TopGO - How to return number of genes associated with each GO term?
topgo
8.1 years ago
kleona3
• 0
0
votes
1
reply
1.1k
views
selection of interesting genes for a KS test in TopGO
topgo
updated 8.1 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.1 years ago by
l.santiago
• 0
0
votes
1
reply
1.2k
views
Filtering Tophat/cufflinks data for GSEA with topGO
topGO
tophat
kolmogorov-smirnov test
updated 8.2 years ago by
James W. MacDonald
68k • written 8.2 years ago by
aaronrosenstein
• 0
2
votes
1
reply
2.6k
views
How to get genes corresponding to a GO term from topGOData object?
topGO
microarray
R
gene ontology
updated 8.2 years ago by
mt1022
▴ 10 • written 9.5 years ago by
rishi.dasroy
▴ 20
0
votes
5
replies
2.6k
views
topGO error using annFUN.org
software error
go
topgo
8.2 years ago
Florian Pauler
• 0
2
votes
2
replies
5.1k
views
topGO gene names/ensembl IDs
topgo
biomart
deseq2
gene ontology
updated 8.3 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.3 years ago by
krc3004
▴ 10
0
votes
1
reply
1.2k
views
How to update the list of genes mapped to GO terms in the topGO object?
topgo
go
8.5 years ago
colaneri
▴ 30
1
vote
2
replies
1.7k
views
Error when using the showGroupDensity function in topGO
topGO
updated 8.5 years ago by
James W. MacDonald
68k • written 8.5 years ago by
colaneri
▴ 30
0
votes
1
reply
1.3k
views
understanding topGO enrichment
topgo
8.5 years ago
michael.steffen
▴ 20
0
votes
3
replies
3.1k
views
topGO - treating up- and down-regulated genes separately
topGO
GSEA
pathway analysis
updated 8.5 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.5 years ago by
predeus
• 0
0
votes
6
replies
2.3k
views
How are feasible genes determined in topGO
topgo
updated 8.5 years ago by
James W. MacDonald
68k • written 8.5 years ago by
michael.steffen
▴ 20
0
votes
0
replies
1.1k
views
topGO plotting options: It is possible to control the number of nodes in the DAG plot according with their p values?
topgo
DAG
8.5 years ago
colaneri
▴ 30
5
votes
1
reply
1.6k
views
topGO under-representation table
topGO
GO
8.6 years ago • updated 8.5 years ago
beachboarder900
▴ 40
0
votes
0
replies
2.0k
views
Problem when using topGO for RNAseq data: The number of annotated genes for GO terms changes according to the number of genes in the gene-background-…
topGO
gene ontolology
rnaseq
8.5 years ago
colaneri
▴ 30
0
votes
1
reply
2.7k
views
clusterProlifer: plotGOgraph() error with gseGO() result
clusterprofiler
gseGO
plotGOgraph()
topGO
updated 8.5 years ago by
Guangchuang Yu
★ 1.2k • written 8.6 years ago by
cjsifuen
• 0
0
votes
4
replies
2.3k
views
topGO: No adjacent nodes prevents BP analysis
topGO
8.7 years ago
hollinew
• 0
1
vote
2
replies
3.2k
views
topGO for Gene Ontology and Gene Set enrichment
topgo
gene ontology
gene set enrichment
rna-seq
bioinformatics
updated 8.7 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.9 years ago by
fromhj304
▴ 10
2
votes
4
replies
2.5k
views
topGO crashes with ' argument "annotationFun" is missing, with no default'
bug
topGO
updated 8.8 years ago by
James W. MacDonald
68k • written 8.8 years ago by
Philip Lijnzaad
▴ 160
0
votes
2
replies
3.0k
views
clusterProfiler - interpretation of plotGOgraph
clusterprofiler
topgo
8.9 years ago
Jane Merlevede
▴ 90
0
votes
0
replies
771
views
How to use combineResults from topGO package?
topGO
topgo
9.0 years ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
2.3k
views
Pathview & topGO
R
GO
topGO
pathview
updated 9.1 years ago by
Luo Weijun
★ 1.6k • written 9.1 years ago by
cabezasdelafuented
▴ 10
0
votes
2
replies
1.6k
views
topgo rnaseq error
topgo
rnaseq
9.1 years ago
tarek.mohamed
▴ 10
0
votes
2
replies
2.9k
views
topGO fro RNA-seq
topgo
rnaseq
9.1 years ago
tarek.mohamed
▴ 10
0
votes
1
reply
1.3k
views
TopGO Drosophila ananassae
go enrichment
topgo
d.ananassae
updated 9.2 years ago by
James W. MacDonald
68k • written 9.2 years ago by
koeniger
▴ 10
211 results • Page
2 of 5
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Comment: Heatmap of the Count Matrix
by
ArnulfoByrd
• 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics
by
James W. MacDonald
68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF
by
James W. MacDonald
68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
by
Michael Love
43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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