Extended Human Microbiome Project (HMP1-II)

Ciataion

If you use the data software, please cite: Lloyd-Price, Jason, et al. "Strains, functions and dynamics in the expanded Human Microbiome Project." Nature volume 550, pages61–66(2017).

If you have questions, please direct it to :

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Contents

• Description
• Requirements
• Load data
• Initial analyses
  • Input Files
  • Output Files
  • Run analysis
• Visualization

Description

The human microbiome plays a key role in health and disease, and the NIH Human Microbiome Project (HMP) has provided one of the broadest overview of the normal diversity of microbes and their function in the absence of dysbiosis. In this work, we have greatly expanded previously available metagenomic profiles to include deep sequencing of over 2,000 samples drawn from 7 different body sites over three time points in a population of 100 individuals. New analyses include taxonomic profiles of the viral and eukaryotic components of the body-wide microbiota (in addition to bacteria and archaea), strain identification and tracking, longitudinal dynamics, and organism-specific metabolic reconstruction, in addition to expansions of previously available gene catalogs and metagenomic assemblies. The "second wave" of data from the first HMP cohort, the HMP1-II, thus provides unprecedented depth of structural and functional profiling of normal human microbial diversity.

Here, we apply several new techniques on analyzing these data including comics community detection along with visualizing data.

Requirements

Data are available in the R data package GWDBB.

Our visualization requires R omicsPattern.

Omice community detection require Python package m2clust.

Load data

Initial analyses