Bioconductor RCy3

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igraph KEGGgraph RCy3 GraphNEL

5 months ago • updated 4 months ago Arindam ▴ 80

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861

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RCy3

9 months ago Matthew Thornton ▴ 380

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511

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Cytoscape RCy3 RCy

updated 14 months ago by alex.pico ▴ 30 • written 14 months ago by David R ▴ 90

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Network RCy3

updated 14 months ago by alex.pico ▴ 30 • written 14 months ago by David R ▴ 90

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747

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RCy3 Cytohubba

updated 14 months ago by alex.pico ▴ 30 • written 14 months ago by jzhan067 ▴ 10

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Cytoscape RCy3 Networkvisualization WGCNA

21 months ago Ortega-C ▴ 10

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981

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RCy3

updated 2.1 years ago by alex.pico ▴ 30 • written 2.1 years ago by adR ▴ 40

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GEOquery CancerData limma RCy3 CancerInSilico

updated 3.3 years ago by Steve Lianoglou ★ 13k • written 3.3 years ago by Caitlin ▴ 50

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rcy3

updated 4.2 years ago by alex.pico ▴ 30 • written 5.2 years ago by hanna226613 ▴ 10

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Cytoscape Pathways Wikipathways rWikiPathways RCy3

4.2 years ago Emilia ▴ 40

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949

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RCy3 Cytoscape R Newick Bioconductor

updated 4.2 years ago by alex.pico ▴ 30 • written 4.6 years ago by ellisjc • 0

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RCy3 Cytoscape Rgraphviz GOstats

5.8 years ago Matthew Thornton ▴ 380

12 results • Page 1 of 1

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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k

No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…

Votes

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

Answer: Group-specific condition effects with individuals nested: matrix is not full ra

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