Showing : RCy3 • reset
2
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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
10 weeks ago Matthew Thornton ▴ 370
1
vote
1
reply
348
views
Going back to default settings in RCy3
Cytoscape RCy3 RCy
updated 6 months ago by ▴ 20 • written 7 months ago by ▴ 90
1
vote
1
reply
960
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 6 months ago by ▴ 20 • written 7 months ago by ▴ 90
1
vote
1
reply
410
views
Cytohubba in RCY3
RCy3 Cytohubba
updated 6 months ago by ▴ 20 • written 7 months ago by ▴ 10
3
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7
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1.4k
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
14 months ago Ortega-C ▴ 10
1
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1
reply
712
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how to call an app from Cytoscape using R?
RCy3
updated 18 months ago by ▴ 20 • written 18 months ago by ▴ 30
2
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3
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1.4k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 2.7 years ago by ★ 13k • written 2.7 years ago by ▴ 50
1
vote
2
replies
957
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RCy3 Cytoscape package question
rcy3
updated 3.6 years ago by ▴ 20 • written 4.6 years ago by ▴ 10
1
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3
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1.4k
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loadTableData function from RCy3 returns "Failed to load data: Provided key columns do not contain any matches"
Cytoscape Pathways Wikipathways rWikiPathways RCy3
3.6 years ago Emilia ▴ 30
0
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1
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810
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Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 3.6 years ago by ▴ 20 • written 4.0 years ago by • 0
3
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4
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1.5k
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Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
5.2 years ago Matthew Thornton ▴ 370
11 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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