Functional Profiling KEGG eggNOG & HUMAnN — Hands-on

Learn how to transform metagenomic and metatranscriptomic reads into interpretable functional profiles using KEGG, eggNOG and HUMAnN. This module covers gene family quantification, pathway reconstruction, stratified contributions, normalisation strategies and statistical summaries for microbiome function and resistome context.

Functional Profiling KEGG eggNOG & HUMAnN

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Session Index

Session 1 — Functional Profiling Concepts & Databases Session 2 — HUMAnN Pipelines & Gene Family Tables Session 3 — Pathway Reconstruction, Stratification & Statistics Session 4 — Mini Capstone: Functional Microbiome Report

Session 1

Fee: Rs 8800

Functional Profiling Concepts & Databases

From reads to functions in microbiome studies

gene families vs pathways vs modules linking taxonomy and function applications in AMR and ecology

Reference databases for functional annotation

KEGG orthology and pathway maps eggNOG and orthologous groups UniRef and other gene catalogues

Inputs and outputs expected by HUMAnN style workflows

preprocessed and decontaminated reads gene family, pathway and stratified tables file formats and naming conventions

Session 2

Fee: Rs 11800

HUMAnN Pipelines & Gene Family Tables

Running HUMAnN style functional profiling

mapping to pangenome and translated search using preprocessed metagenomic reads log and quality checks

Gene family tables and normalisation options

cpm and reads per kilobase style metrics copies per million and relative abundance handling zeros and sparse matrices

Stratified outputs and linking to taxa

unstratified vs stratified tables which taxa carry which pathways exporting to R or Python for analysis

Session 3

Fee: Rs 14800

Pathway Reconstruction, Stratification & Statistics

Pathway level profiles and completeness

mapping gene families to KEGG pathways module and pathway completeness scores filtering low confidence pathways

Differential functional abundance and enrichment

compositional aware tests for functions enrichment of pathways across groups multi testing adjustment and interpretation

Visualisation of functional profiles and stratified contributions

heatmaps and pathway barplots stacked plots by taxa and function linking function to metadata and outcomes

Session 4

Fee: Rs 18800

Mini Capstone: Functional Microbiome Report

End to end functional profiling for a microbiome dataset

theory plus guided practical

Summarising key pathways and contributing taxa

short chain fatty acid pathways AMR and virulence related functions clinical and environmental interpretation

Deliverables: gene family table, pathway summaries and report

normalised function tables R or Python analysis notebook PDF or HTML functional microbiome report

PDF

Functional Profiling KEGG eggNOG & HUMAnN Training | Microbiome Pathways & Gene Families

Functional Profiling KEGG eggNOG & HUMAnN — Hands-on