Showing : Cytoscape • reset
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Going back to default settings in RCy3
Cytoscape RCy3 RCy
updated 21 months ago by ▴ 30 • written 22 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
2.4 years ago Ortega-C ▴ 10
0
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0
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1.5k
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
2.7 years ago gianni.drm • 0
0
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1
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1.1k
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Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 4.8 years ago by ▴ 30 • written 5.2 years ago by • 0
3
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4
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2.0k
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Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
6.4 years ago Matthew Thornton ▴ 380
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0
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Exploring upstream regulators (transcription factors, drugs, etc) of transcripts in R
microarray bioconductor cytoscape mapfromtranscripts
7.0 years ago lm795 ▴ 10
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1.5k
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Help with generating network from gene expression data
gene expression network cytoscape
7.7 years ago torgeirous • 0
6
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8
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11k
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WGCNA export to cytoscape
wgcna cytoscape
updated 7.8 years ago by ▴ 60 • written 8.4 years ago by ▴ 60
0
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1
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1.7k
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WGNA export to external software
WGCNA network visualization external software cytoscape
updated 8.0 years ago by ★ 3.0k • written 8.0 years ago by • 0
9 results • Page 1 of 1
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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