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RCy3
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3
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7
replies
1.1k
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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
replies
1.4k
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
vote
3
replies
1.2k
views
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
replies
1.2k
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
Steve Lianoglou
★ 13k • written 2.4 years ago by
Caitlin
▴ 50
1
vote
2
replies
852
views
RCy3 Cytoscape package question
rcy3
updated 3.3 years ago by
alex.pico
▴ 20 • written 4.3 years ago by
hanna226613
▴ 10
1
vote
1
reply
281
views
Cytohubba in RCY3
RCy3
Cytohubba
updated 3 months ago by
alex.pico
▴ 20 • written 3 months ago by
jzhan067
▴ 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
alex.pico
▴ 20 • written 3.8 years ago by
ellisjc
• 0
1
vote
1
reply
579
views
how to call an app from Cytoscape using R?
RCy3
updated 15 months ago by
alex.pico
▴ 20 • written 15 months ago by
adR
▴ 30
1
vote
1
reply
813
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network
RCy3
updated 3 months ago by
alex.pico
▴ 20 • written 4 months ago by
David R
▴ 90
1
vote
1
reply
257
views
Going back to default settings in RCy3
Cytoscape
RCy3
RCy
updated 3 months ago by
alex.pico
▴ 20 • written 3 months ago by
David R
▴ 90
10 results • Page
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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.
Votes
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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