Showing : cytoscape • reset
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Going back to default settings in RCy3
Cytoscape RCy3 RCy
updated 3 months ago by ▴ 20 • written 3 months ago by ▴ 90
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
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
14 months ago gianni.drm • 0
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1
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720
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Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 3.3 years ago by ▴ 20 • written 3.8 years ago by • 0
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4
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1.4k
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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
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Exploring upstream regulators (transcription factors, drugs, etc) of transcripts in R
microarray bioconductor cytoscape mapfromtranscripts
5.5 years ago lm795 ▴ 10
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Help with generating network from gene expression data
gene expression network cytoscape
6.3 years ago torgeirous • 0
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WGCNA export to cytoscape
wgcna cytoscape
updated 6.3 years ago by ▴ 60 • written 6.9 years ago by ▴ 60
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1
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1.2k
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WGNA export to external software
WGCNA network visualization external software cytoscape
updated 6.6 years ago by ★ 3.0k • written 6.6 years ago by • 0
9 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
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Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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