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RCy3
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reset
3
votes
4
replies
1.3k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3
Cytoscape
Rgraphviz
GOstats
4.9 years ago
Matthew Thornton
▴ 350
1
vote
2
replies
830
views
RCy3 Cytoscape package question
rcy3
updated 3.3 years ago by
alex.pico
▴ 20 • written 4.2 years ago by
hanna226613
▴ 10
1
vote
1
reply
247
views
Cytohubba in RCY3
RCy3
Cytohubba
updated 12 weeks ago by
alex.pico
▴ 20 • written 3 months ago by
jzhan067
▴ 10
1
vote
1
reply
233
views
Going back to default settings in RCy3
Cytoscape
RCy3
RCy
updated 11 weeks ago by
alex.pico
▴ 20 • written 3 months ago by
David R
▴ 90
3
votes
7
replies
1.1k
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
10 months ago
Ortega-C
▴ 10
1
vote
1
reply
549
views
how to call an app from Cytoscape using R?
RCy3
updated 14 months ago by
alex.pico
▴ 20 • written 14 months ago by
adR
▴ 30
1
vote
1
reply
784
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network
RCy3
updated 11 weeks ago by
alex.pico
▴ 20 • written 3 months ago by
David R
▴ 90
2
votes
3
replies
1.2k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery
CancerData
limma
RCy3
CancerInSilico
updated 2.4 years ago by
Steve Lianoglou
★ 13k • written 2.4 years ago by
Caitlin
▴ 50
1
vote
3
replies
1.2k
views
loadTableData function from RCy3 returns "Failed to load data: Provided key columns do not contain any matches"
Cytoscape
Pathways
Wikipathways
rWikiPathways
RCy3
3.3 years ago
Emilia
▴ 30
0
votes
1
reply
706
views
Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3
Cytoscape
R
Newick
Bioconductor
updated 3.3 years ago by
alex.pico
▴ 20 • written 3.7 years ago by
ellisjc
• 0
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
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This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
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James W. MacDonald
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It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
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by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
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DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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