Showing : rcy3 • reset
3
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7
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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
11 months ago Ortega-C ▴ 10
3
votes
4
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1.3k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
4.9 years ago Matthew Thornton ▴ 350
1
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3
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1.2k
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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
3.4 years ago • updated 3.3 years ago Emilia ▴ 30
2
votes
3
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1.2k
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 2.4 years ago by ★ 13k • written 2.4 years ago by ▴ 50
1
vote
2
replies
850
views
RCy3 Cytoscape package question
rcy3
updated 3.3 years ago by ▴ 20 • written 4.3 years ago by ▴ 10
1
vote
1
reply
279
views
Cytohubba in RCY3
RCy3 Cytohubba
updated 3 months ago by ▴ 20 • written 3 months ago by ▴ 10
0
votes
1
reply
720
views
Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 3.3 years ago by ▴ 20 • written 3.7 years ago by • 0
1
vote
1
reply
576
views
how to call an app from Cytoscape using R?
RCy3
updated 15 months ago by ▴ 20 • written 15 months ago by ▴ 30
1
vote
1
reply
811
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How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 3 months ago by ▴ 20 • written 3 months ago by ▴ 90
1
vote
1
reply
252
views
Going back to default settings in RCy3
Cytoscape RCy3 RCy
updated 3 months ago by ▴ 20 • written 3 months ago by ▴ 90
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Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Answer: blockwiseModule crashes in the end and doesn't generate modules by xaweh28128 • 0
Test your word skills and see if you can crack the code in today's Wordle puzzle. [Nytimes wordle](https://wordlenytimes.net/quordle-game/)…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you Michael for your attention to my question. I am truly grateful. I subsetted the data using lines of codes to include only the g…
Votes
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
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