Showing : RCy3 • reset
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
5.0 years ago Matthew Thornton ▴ 350
1
vote
2
replies
863
views
RCy3 Cytoscape package question
rcy3
updated 3.4 years ago by ▴ 20 • written 4.3 years ago by ▴ 10
1
vote
1
reply
295
views
Cytohubba in RCY3
RCy3 Cytohubba
updated 3 months ago by ▴ 20 • written 4 months ago by ▴ 10
1
vote
1
reply
269
views
Going back to default settings in RCy3
Cytoscape RCy3 RCy
updated 3 months ago by ▴ 20 • written 4 months ago by ▴ 90
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
11 months ago Ortega-C ▴ 10
1
vote
1
reply
593
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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
831
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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 4 months ago by ▴ 90
2
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3
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1.3k
views
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 2.5 years ago by ▴ 50
1
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3
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1.3k
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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 Emilia ▴ 30
0
votes
1
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731
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Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 3.4 years ago by ▴ 20 • written 3.8 years ago by • 0
10 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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