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cytoscape / cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js
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16s micrbiome network analysis #59

Closed marwa38 closed 2 years ago

marwa38 commented 2 years ago

Hello

I am new to cytoscape.

Could you please share with me a tutorial or simple steps to how to do network analysis of a 16s rRNA microbiome data I have collected?

Thanks very much Marwa

AlexanderPico commented 2 years ago

Hi. All the available tutorials are found on the wiki page of this repo. There are none specific to 16s rRNA that I’m aware of. You might try asking biology questions on a forum of bioinformatics like BioStars.

marwa38 commented 2 years ago

Thank for your prompt reply. @AlexanderPico Why I am asking about 16s as the inputs in the tutorials are network but I have phyloseq object which contains taxonomy table and features table (ASVs), have you heard about using different inputs before? phyloseq people don't know how to do so in cytoscape? this will be so helfpul

AlexanderPico commented 2 years ago

I'm not familiar with phyloseq or ASVs. The only thing I've worked with involving phylogenetic trees is this R-based conversion of the Newick tree format to Cytoscape networks: https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Phylogenetic-trees.nb.html.

marwa38 commented 2 years ago

Thanks very much @AlexanderPico