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RCy3
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reset
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272
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Going back to default settings in RCy3
Cytoscape
RCy3
RCy
updated 3 months ago by
alex.pico
▴ 20 • written 4 months ago by
David R
▴ 90
1
vote
1
reply
836
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network
RCy3
updated 3 months ago by
alex.pico
▴ 20 • written 4 months ago by
David R
▴ 90
1
vote
1
reply
297
views
Cytohubba in RCY3
RCy3
Cytohubba
updated 3 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
601
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
869
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
734
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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Replies
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma
by
James W. MacDonald
65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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