Functional Profiling (HUMAnN) & Pathway Inference — Hands-on

Build end-to-end functional profiling workflows that convert shotgun metagenomic reads into biologically meaningful pathways. You'll run HUMAnN with proper references, perform gene-family regrouping to KO/EC/Rhea, quantify pathway abundance and coverage (MetaCyc/KEGG) , and apply robust compositional statistics for differential pathway analysis. Deliver publication-ready figures and reproducible reports.

Functional Profiling (HUMAnN) & Pathway Inference

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Session Index

Session 1 — Concepts, References & Setup Session 2 — HUMAnN Gene Families Workflow Session 3 — Pathway Inference & Normalization Session 4 — DA, Visualization & Reporting

Session 1

Fee: Rs 8800

Concepts, References & Setup

Functional profiling fundamentals

community vs. stratified reads → genes → pathways abundance vs. coverage

Databases & indexing

UniRef90/50 MetaCyc / KEGG mapping ChocoPhlAn + MetaPhlAn link

Environment & reproducibility

conda / containers workflow scaffolding provenance & logs

Session 2

Fee: Rs 11800

HUMAnN Gene Families Workflow

Preprocessing & stratification

paired-end inputs species-stratified tables unclassified fraction

Search & quantification

Bowtie2/DIAMOND stages UniRef90/50 outputs TPM/RPK interpretation

Regrouping & renormalization

KO / EC / eggNOG copy-number caveats per-million scaling

Session 3

Fee: Rs 14800

Pathway Inference & Normalization

Pathway abundance & coverage

MetaCyc mapping MinPath concepts stratified contributions

Normalization & integration

CLR/rCLR awareness per-sample scaling merge with taxonomy

Quality checks & filters

prevalence & sparsity batch/run effects mock community sanity

Session 4

Fee: Rs 18800

Differential Analysis, Visualization & Reporting

Compositional DA for pathways

ANCOM-BC / ALDEx2 confounders & covariates effect sizes & FDR

Visualization & interpretation

Sankey/chord/heatmaps rank plots & volcano species contributions

Reproducible outputs

Quarto / R Markdown tables, figures & model cards data dictionary & code

PDF

Functional Profiling (HUMAnN) & Pathway Inference Training | UniRef→KO/EC, MetaCyc/KEGG, DA & Reporting

Functional Profiling (HUMAnN) & Pathway Inference — Hands-on