Functional profiling

Compare microbial pathway and gene-family abundance across cohorts, keeping measured functions distinct from inferred functional potential.

Research question

Which microbial pathways or gene families differ between communities, and are those functions measured directly or inferred from taxonomy?

Who this is for

Microbiome researchers moving from "who is there" to "what they can do"
Teams comparing functional potential across treatment or environment groups
Analysts linking functional findings back to contributing taxa

Data requirements

Data	Required	Purpose
Pathway or gene-family table (pathways × samples)	Yes	Functional abundance
Sample metadata with a group column	No	Cohort contrast between groups

Workflow

Upload pathway table (+ metadata) → Pathway abundance
  → Cohort comparison (optional)
  → Review top pathways and log2 fold changes
  → AI interpretation

Step 1 — Pathway abundance

Run the Function analysis to compute pathway relative abundance and the most abundant pathways across samples. The inference field records whether values are measured genes or inferred potential.

Step 2 — Cohort comparison

With a grouping column, the pipeline reports per-pathway log2 fold change and BH-corrected significance between two cohorts.

Expected outputs

Top pathways with mean relative abundance
Cohort contrast with log2 fold change and q-values
Explicit measured-vs-inferred provenance