Functional Profiling
====================

Goal
----

Quantify transcript abundance mapped to gene families or pathways.

Tools
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- HUMAnN3 (with metatranscriptome support)
- SAMSA2
- Custom gene catalogs with featureCounts

Normalization
-------------

Use CPM or TPM for expression; aggregate to pathways for biological interpretation.

Outputs
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- pathway_abundance.tsv
- gene_families.tsv