GitHub - ohlab/longitudinal (original) (raw)

LONGITUDINAL SKIN METAGENOMICS DATA REPOSITORY

This repository contains data underlying analyses as described in:

Temporal Stability of the Human Skin Microbiome

Julia Oh, Allyson L. Byrd, Morgan Park, Heidi H. Kong, and Julia A. Segre Cell 165, 854–866 (2016)

A brief description of the contents:

Supplemental_data/ samples.txt Sequencing statistics/metadata for samples used in the study classifications.txt Species-level taxonomic classifications and diversity estimates diversity.txt Diversity estimates, species diversity_eukvir.txt Number of species observed, eukaryotic viruses diversity_phage.txt Number of species observed, phage

thetas.species.txt Theta calculations for all pairwise comparisons of samples, species thetas.genus.txt Theta calculations for all pairwise comparisons of samples, genus thetas.family.txt Theta calculations for all pairwise comparisons of samples, family thetas.phylum.txt Theta calculations for all pairwise comparisons of samples, phylum thetas.kingdom.txt Theta calculations for all pairwise comparisons of samples, kingdom thetas.phage.txt Theta calculations for all pairwise comparisons of samples, phage thetas.eukvir.txt Theta calculations for all pairwise comparisons of samples, eukaryotic viruses

transient.txt Species classified as transient or not within abundance groups randomforests.xlsx Random forests output

pacnes_strains.txt Relative abundance of Propionibacterium acnes strains pacnes_genes.txt Presence/absence of Propionibacterium acnes gene clusters sepi_strains.txt Relative abundance of Staphylococcus epidermidis strains sepi_genes.txt Presence/absence of gene clusters of Staphylococcus epidermidis gene clusters

Databases_used/ The reference genome databases used for this study, including bacteria, fungi, archaea, and viruses and instructions for download and making bowtie indices