Network Analysis — Co-occurrence & Community Modules — Hands-on

Learn how to move from abundance tables to interpretable microbiome networks. This module covers co occurrence and association inference methods, construction and visualization of microbiome graphs, detection of community modules and hubs, and how to relate network structure to ecological, clinical and AMR endpoints.

Network Analysis — Co-occurrence & Community Modules

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Session Index

Session 1 — Network Concepts & Data Preparation Session 2 — Co-occurrence & Association Inference Session 3 — Community Modules, Hubs & Interpretation Session 4 — Mini Capstone: Co-occurrence Network Story

Session 1

Fee: Rs 8800

Network Concepts & Data Preparation

Why networks for microbiome data

co occurrence as hypothesis generator taxa as nodes, edges as associations ecology and AMR surveillance context

Preparing feature tables for network analysis

filtering low prevalence and low abundance taxa handling zeros and sparsity choice of taxonomic level (ASV vs genus)

Toolchain overview for microbiome networks

R (phyloseq, vegan, igraph) Python (pandas, networkx) Cytoscape and web based visual tools

Session 2

Fee: Rs 11800

Co-occurrence & Association Inference

Simple correlation and its limitations

Spearman and Pearson correlations spurious edges from compositionality multiple testing across pairs

SparCC, SPIEC-EASI and related methods

SparCC style correlation for compositional data SPIEC EASI graphical models overview FlashWeave and fast association tools

From association matrices to network objects

thresholding and sparsity control signed and weighted edges exporting to igraph or Cytoscape formats

Session 3

Fee: Rs 14800

Community Modules, Hubs & Interpretation

Community detection and modules

Louvain, Leiden and related algorithms module membership and modularity interpreting ecological guilds

Centrality and key taxa identification

degree, betweenness and closeness hub and connector taxa concepts overlaying AMR or functional labels

Visualisation and linking to metadata

layout choices and aesthetic mapping colouring by module or taxonomic group associating modules with sample traits

Session 4

Fee: Rs 18800

Mini Capstone: Co-occurrence Network Story

Designing a network analysis for one dataset

guided theory plus practical

From feature table to network, modules and hubs

run one association method (for example SparCC or SPIEC EASI) build network and detect modules identify key hub taxa

Deliverables: network figures, tables and interpretation

Cytoscape or R based network plots module and centrality summary tables short narrative linking modules to biology or AMR

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Network Analysis — Co-occurrence & Community Modules Training | Microbiome Networks & Hubs

Network Analysis — Co-occurrence & Community Modules — Hands-on