Bioconductor Rcy3

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1.4k

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RCy3 Cytoscape Rgraphviz GOstats

5.0 years ago Matthew Thornton ▴ 350

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1.2k

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Cytoscape RCy3 Networkvisualization WGCNA

11 months ago Ortega-C ▴ 10

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1.3k

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GEOquery CancerData limma RCy3 CancerInSilico

updated 2.5 years ago by Steve Lianoglou ★ 13k • written 2.5 years ago by Caitlin ▴ 50

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609

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RCy3

updated 15 months ago by alex.pico ▴ 20 • written 15 months ago by adR ▴ 30

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849

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Network RCy3

updated 4 months ago by alex.pico ▴ 20 • written 4 months ago by David R ▴ 90

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279

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Cytoscape RCy3 RCy

updated 4 months ago by alex.pico ▴ 20 • written 4 months ago by David R ▴ 90

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302

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RCy3 Cytohubba

updated 4 months ago by alex.pico ▴ 20 • written 4 months ago by jzhan067 ▴ 10

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878

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rcy3

updated 3.4 years ago by alex.pico ▴ 20 • written 4.3 years ago by hanna226613 ▴ 10

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1.3k

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Cytoscape Pathways Wikipathways rWikiPathways RCy3

3.4 years ago Emilia ▴ 30

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739

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RCy3 Cytoscape R Newick Bioconductor

updated 3.4 years ago by alex.pico ▴ 20 • written 3.8 years ago by ellisjc • 0

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Comment: Cannot connect to ExperimentHub server by Jiayu • 0

Many thanks and it also resolved the same issue for me!

Comment: Help with running egsea() by Chris • 0

I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…

Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0

Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…

Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k

sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…

Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k

I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?

Votes

A: Error in DESeqDataSet : some values in assay are not integers

Answer: Cannot connect to ExperimentHub server

Answer: confused with tximport counts abundance using salmon input

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call

Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu

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Popular Question to Gyan Prakash Mishra ▴ 10