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rcy3
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reset
1
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903
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KEGGgraph result difference
igraph
KEGGgraph
RCy3
GraphNEL
16 months ago • updated 15 months ago
Arindam
▴ 80
2
votes
2
replies
1.4k
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
20 months ago
Matthew Thornton
▴ 390
1
vote
1
reply
760
views
Going back to default settings in RCy3
Cytoscape
RCy3
RCy
updated 2.1 years ago by
alex.pico
▴ 30 • written 2.1 years ago by
David R
▴ 90
1
vote
1
reply
1.6k
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network
RCy3
updated 2.1 years ago by
alex.pico
▴ 30 • written 2.1 years ago by
David R
▴ 90
1
vote
1
reply
1.4k
views
Cytohubba in RCY3
RCy3
Cytohubba
updated 2.1 years ago by
alex.pico
▴ 30 • written 2.1 years ago by
jzhan067
▴ 10
3
votes
7
replies
2.7k
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
2.7 years ago
Ortega-C
▴ 10
1
vote
1
reply
1.3k
views
how to call an app from Cytoscape using R?
RCy3
updated 3.0 years ago by
alex.pico
▴ 30 • written 3.0 years ago by
adR
▴ 40
2
votes
3
replies
2.3k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery
CancerData
limma
RCy3
CancerInSilico
updated 4.2 years ago by
Steve Lianoglou
★ 13k • written 4.2 years ago by
Caitlin
▴ 50
1
vote
2
replies
1.5k
views
RCy3 Cytoscape package question
rcy3
updated 5.1 years ago by
alex.pico
▴ 30 • written 6.1 years ago by
hanna226613
▴ 10
1
vote
3
replies
2.0k
views
loadTableData function from RCy3 returns "Failed to load data: Provided key columns do not contain any matches"
Cytoscape
Pathways
Wikipathways
rWikiPathways
RCy3
5.1 years ago
Emilia
▴ 40
0
votes
1
reply
1.2k
views
Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3
Cytoscape
R
Newick
Bioconductor
updated 5.1 years ago by
alex.pico
▴ 30 • written 5.5 years ago by
ellisjc
• 0
3
votes
4
replies
2.1k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3
Cytoscape
Rgraphviz
GOstats
6.7 years ago
Matthew Thornton
▴ 390
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Hugo Gruson
• 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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