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Cytoscape
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Going back to default settings in RCy3
Cytoscape
RCy3
RCy
updated 4 months ago by
alex.pico
▴ 20 • written 4 months ago by
David R
▴ 90
3
votes
7
replies
1.2k
views
"Degree values are the same for all nodes in a network imported from WGCNA to Cytoscape using RCy3. Seeking insights and potential causes."
Cytoscape
RCy3
Networkvisualization
WGCNA
11 months ago
Ortega-C
▴ 10
0
votes
0
replies
826
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
15 months ago
gianni.drm
• 0
0
votes
1
reply
739
views
Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3
Cytoscape
R
Newick
Bioconductor
updated 3.4 years ago by
alex.pico
▴ 20 • written 3.8 years ago by
ellisjc
• 0
3
votes
4
replies
1.4k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3
Cytoscape
Rgraphviz
GOstats
5.0 years ago
Matthew Thornton
▴ 350
1
vote
0
replies
1.7k
views
Exploring upstream regulators (transcription factors, drugs, etc) of transcripts in R
microarray
bioconductor
cytoscape
mapfromtranscripts
5.6 years ago
lm795
▴ 10
0
votes
0
replies
1.0k
views
Help with generating network from gene expression data
gene expression
network
cytoscape
6.3 years ago
torgeirous
• 0
6
votes
8
replies
8.3k
views
WGCNA export to cytoscape
wgcna
cytoscape
updated 6.3 years ago by
harelarik
▴ 60 • written 7.0 years ago by
2323982403
▴ 60
0
votes
1
reply
1.2k
views
WGNA export to external software
WGCNA
network visualization
external software
cytoscape
updated 6.6 years ago by
Peter Langfelder
★ 3.0k • written 6.6 years ago by
je.maxfield
• 0
9 results • Page
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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