Showing : RCy3 • reset
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KEGGgraph result difference
igraph KEGGgraph RCy3 GraphNEL
7 months ago • updated 6 months ago Arindam ▴ 80
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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
11 months ago Matthew Thornton ▴ 380
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Going back to default settings in RCy3
Cytoscape RCy3 RCy
updated 15 months ago by ▴ 30 • written 16 months ago by ▴ 90
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How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 15 months ago by ▴ 30 • written 16 months ago by ▴ 90
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873
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Cytohubba in RCY3
RCy3 Cytohubba
updated 15 months ago by ▴ 30 • written 16 months ago by ▴ 10
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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
23 months ago Ortega-C ▴ 10
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how to call an app from Cytoscape using R?
RCy3
updated 2.3 years ago by ▴ 30 • written 2.3 years ago by ▴ 40
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 3.4 years ago by ★ 13k • written 3.4 years ago by ▴ 50
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RCy3 Cytoscape package question
rcy3
updated 4.3 years ago by ▴ 30 • written 5.3 years ago by ▴ 10
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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
4.4 years ago • updated 4.3 years ago Emilia ▴ 40
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Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 4.3 years ago by ▴ 30 • written 4.8 years ago by • 0
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Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
6.0 years ago • updated 5.9 years ago Matthew Thornton ▴ 380
12 results • Page 1 of 1
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Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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