Bioconductor RCy3

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igraph KEGGgraph RCy3 GraphNEL

16 months ago • updated 15 months ago Arindam ▴ 80

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RCy3

20 months ago Matthew Thornton ▴ 390

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Cytoscape RCy3 RCy

updated 2.0 years ago by alex.pico ▴ 30 • written 2.1 years ago by David R ▴ 90

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Network RCy3

updated 2.0 years ago by alex.pico ▴ 30 • written 2.1 years ago by David R ▴ 90

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RCy3 Cytohubba

updated 2.1 years ago by alex.pico ▴ 30 • written 2.1 years ago by jzhan067 ▴ 10

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Cytoscape RCy3 Networkvisualization WGCNA

2.7 years ago Ortega-C ▴ 10

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RCy3

updated 3.0 years ago by alex.pico ▴ 30 • written 3.0 years ago by adR ▴ 40

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GEOquery CancerData limma RCy3 CancerInSilico

updated 4.2 years ago by Steve Lianoglou ★ 13k • written 4.2 years ago by Caitlin ▴ 50

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rcy3

updated 5.1 years ago by alex.pico ▴ 30 • written 6.0 years ago by hanna226613 ▴ 10

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Cytoscape Pathways Wikipathways rWikiPathways RCy3

5.1 years ago Emilia ▴ 40

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RCy3 Cytoscape R Newick Bioconductor

updated 5.1 years ago by alex.pico ▴ 30 • written 5.5 years ago by ellisjc • 0

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RCy3 Cytoscape Rgraphviz GOstats

6.7 years ago Matthew Thornton ▴ 390

12 results • Page 1 of 1

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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0

Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k

Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…

Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

You just need the mouse identifier (controls baseline) and the group specific allelic effect.

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0

Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…

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A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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