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rcy3
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reset
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277
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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
1
vote
1
reply
847
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network
RCy3
updated 4 months ago by
alex.pico
▴ 20 • written 4 months ago by
David R
▴ 90
1
vote
1
reply
300
views
Cytohubba in RCY3
RCy3
Cytohubba
updated 4 months ago by
alex.pico
▴ 20 • written 4 months ago by
jzhan067
▴ 10
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
1
vote
1
reply
606
views
how to call an app from Cytoscape using R?
RCy3
updated 15 months ago by
alex.pico
▴ 20 • written 15 months ago by
adR
▴ 30
2
votes
3
replies
1.3k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery
CancerData
limma
RCy3
CancerInSilico
updated 2.5 years ago by
Steve Lianoglou
★ 13k • written 2.5 years ago by
Caitlin
▴ 50
1
vote
2
replies
875
views
RCy3 Cytoscape package question
rcy3
updated 3.4 years ago by
alex.pico
▴ 20 • written 4.3 years ago by
hanna226613
▴ 10
1
vote
3
replies
1.3k
views
loadTableData function from RCy3 returns "Failed to load data: Provided key columns do not contain any matches"
Cytoscape
Pathways
Wikipathways
rWikiPathways
RCy3
3.4 years ago
Emilia
▴ 30
0
votes
1
reply
738
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
10 results • Page
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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Comment: fgsea significant result
by
Chris
• 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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