Showing : RCy3 • reset
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"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
16 days ago • updated 15 days ago Ortega-C ▴ 10
1
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1
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how to call an app from Cytoscape using R?
RCy3
updated 4 months ago by ▴ 20 • written 4 months ago by ▴ 30
2
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3
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708
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 18 months ago by 13k • written 18 months ago by ▴ 50
1
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2
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RCy3 Cytoscape package question
rcy3
updated 2.4 years ago by ▴ 20 • written 3.4 years ago by ▴ 10
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3
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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
2.5 years ago • updated 2.4 years ago Emilia ▴ 30
0
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Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 2.4 years ago by ▴ 20 • written 2.9 years ago by • 0
3
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4
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Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
4.0 years ago Matthew Thornton ▴ 350
7 results • Page 1 of 1
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Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
Sure, noted.
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would do the job.
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by ansleyharralson • 0
Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.
Votes
WGCNA coupled with differential expression analysis: question about baseline module detection
WGCNA with paired samples
Comment: Question on constructing design matrix and defining contrasts for analysis
Comment: Question on constructing design matrix and defining contrasts for analysis
Answer: Question on constructing design matrix and defining contrasts for analysis
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