Skip to content

HUMAnN ReNormalize Specifications

Process Details

  • Name: HUMAnN_ReNormalize
  • Process UUID: 50070fa7456847c5952598989ee2dc3e
  • Process Group: Functional Profiling

Overview

HUMAnN ReNormalize is a normalization utility for HUMAnN (The HMP Unified Metabolic Analysis Network) that standardizes TSV files containing functional profiling data. This process renormalizes stratified tables where each level is normalized using the desired normalization scheme, enabling consistent comparison of functional profiles across samples.

This process is implemented in Bash, which invokes HUMAnN's renormalization utility for functional profile standardization.

Key Functionality

  • Table Renormalization: Applies normalization schemes to functional profiling data tables
  • Stratified Data Processing: Handles multi-level stratified tables with appropriate normalization at each level
  • Flexible Normalization Options: Supports multiple normalization methods and modes for different analytical needs

Input/Output Specification

Inputs

Required Inputs

  • Input TSV File
    • Description: Functional profiling table from HUMAnN containing gene families, pathways, or other functional annotations
    • Format: TSV

Outputs

  • Normalized TSV File
    • Description: Renormalized functional profiling table with standardized abundance values
    • Format: TSV

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Normalization Units

    • Description: Choose the method for normalization: cpm for copies per million, relab for relative abundance
    • Available options: cpm (default), relab

  • Normalization Mode

    • Description: Normalize all levels by community or levelwise totals
    • Available options: community (default), levelwise

  • Include special features?

    • Description: Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED
    • Available options: y (default), n

References & Resources

  • Tool Documentation: Contact the team for details on HUMAnN renormalization utility
  • Related Papers: Franzosa, E.A., McIver, L.J., Rahnavard, G., Thompson, L.R., Schirmer, M., Weingart, G., Lipson, K.S., Knight, R., Caporaso, J.G., Segata, N. and Huttenhower, C. (2018). Species-level functional profiling of metagenomes and metatranscriptomes. Nature Methods, 15(11), 962-968.