16s micrbiome network analysis

[marwa38]

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]

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]

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]

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]

Thanks very much @AlexanderPico