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RCy3
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2
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337
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Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
5 days ago • updated 1 day ago
Matthew Thornton
▴ 360
1
vote
1
reply
286
views
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
859
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 5 months ago by
David R
▴ 90
1
vote
1
reply
317
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
12 months ago
Ortega-C
▴ 10
1
vote
1
reply
618
views
how to call an app from Cytoscape using R?
RCy3
updated 16 months ago by
alex.pico
▴ 20 • written 16 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
883
views
RCy3 Cytoscape package question
rcy3
updated 3.4 years ago by
alex.pico
▴ 20 • written 4.4 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
751
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
▴ 360
11 results • Page
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Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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