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cytoscape
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Going back to default settings in RCy3
Cytoscape
RCy3
RCy
updated 15 months ago by
alex.pico
▴ 30 • written 16 months ago by
David R
▴ 90
3
votes
7
replies
2.1k
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
23 months ago
Ortega-C
▴ 10
0
votes
0
replies
1.3k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
2.2 years ago
gianni.drm
• 0
0
votes
1
reply
976
views
Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3
Cytoscape
R
Newick
Bioconductor
updated 4.3 years ago by
alex.pico
▴ 30 • written 4.8 years ago by
ellisjc
• 0
3
votes
4
replies
1.8k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3
Cytoscape
Rgraphviz
GOstats
6.0 years ago • updated 5.9 years ago
Matthew Thornton
▴ 380
1
vote
0
replies
2.2k
views
Exploring upstream regulators (transcription factors, drugs, etc) of transcripts in R
microarray
bioconductor
cytoscape
mapfromtranscripts
6.5 years ago
lm795
▴ 10
0
votes
0
replies
1.3k
views
Help with generating network from gene expression data
gene expression
network
cytoscape
7.3 years ago
torgeirous
• 0
6
votes
8
replies
10k
views
WGCNA export to cytoscape
wgcna
cytoscape
updated 7.3 years ago by
harelarik
▴ 60 • written 7.9 years ago by
2323982403
▴ 60
0
votes
1
reply
1.6k
views
WGNA export to external software
WGCNA
network visualization
external software
cytoscape
updated 7.6 years ago by
Peter Langfelder
★ 3.0k • written 7.6 years ago by
je.maxfield
• 0
9 results • Page
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Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
donnycrimson
• 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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