Network Analysis of Microbiome Data: MicrobiomeAnalyst vs. Cytoscape

Question

[ohtang7]

Dear MicrobiomeAnalyst users,

I'm seeking guidance on conducting correlation network analysis for microbiome data, specifically using 16S and 18S rRNA amplicon sequencing data containing a table of ASVs and their read counts.

I'm considering two tools:

MicrobiomeAnalyst: This web-based tool offers network analysis functionality, eliminating the need for Cytoscape. Cytoscape: While MicrobiomeAnalyst offers other functions like alpha, beta analysis, and correlation analysis, many research articles utilize Cytoscape for network analysis in conjunction with these functions. My questions are:

Disadvantages of using MicrobiomeAnalyst's network analysis: Does it limit visualization of positive/negative correlations? The protocol image only shows nodes, lacking clarity on correlation strength and direction as below...

Experiences with MicrobiomeAnalyst's network analysis: Have users encountered any significant drawbacks compared to Cytoscape? Cytoscape with microbiome data: Are there significant challenges in using Cytoscape with ASV files or metadata for network analysis? Additionally, I'm exploring the MENAP web tool, which employs different from SparCC algorithms for its analysis.

I truly appreciate your insights and advice!

Best regards,

[Mensur Dlakic]

Doing the network analysis takes comparatively less time than gathering the data for it. No matter what anyone tells you, I think the most appropriate application for your purposes is best found by experimentation. It may take half a day or even a whole day, but you will be able to make a more informed decision.