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A mathematical framework to correct for compositionality in microbiome datasets

Published by National Institute of Standards and Technology | National Institute of Standards and Technology | Catalog Last Checked: August 03, 2026 at 03:52 AM | Dataset Last Updated: March 13, 2025
This repository provides the raw data and analysis code used to demonstrate the implementation of a mathematical framework that uses internal standards to correct for compositionally in MGS datasets. Some of the data contained herein was previously published and is reanalyzed in the context of this new framework, while other datasets represent newly analyzed samples. Please refer to the associated publication for further discussion and a full exploration of the results.

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Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
[
  "006:55"
]
contactPoint 
{
  "fn": "Samuel P. Forry",
  "hasEmail": "mailto:samuel.forry@nist.gov"
}
description This repository provides the raw data and analysis code used to demonstrate the implementation of a mathematical framework that uses internal standards to correct for compositionally in MGS datasets. Some of the data contained herein was previously published and is reanalyzed in the context of this new framework, while other datasets represent newly analyzed samples. Please refer to the associated publication for further discussion and a full exploration of the results.
distribution 
[
  {
    "title": "01RawData.zip",
    "mediaType": "application/zip",
    "description": "This compressed folder contains the raw data and preliminary analysis code for analyzing stool samples to explore particular hypotheses arising from the proposed framework. The summarized results (i.e., taxa tables) for each dataset are copied into the '03DataAnalysis/Tabulated Data/' folder.",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/01RawData.zip"
  },
  {
    "title": "00READEME.txt",
    "mediaType": "text/plain",
    "description": "This file contains a plaintext description of the data repository.",
    "downloadURL": "https://data.nist.gov/od/ds/mds2-3760/00README.txt"
  },
  {
    "title": "250211-Analysis.Rmd",
    "mediaType": "application/octet-stream",
    "description": "This file provides the highest level R Markdown code used for analysis of the files in this directory.",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/250211-Analysis.Rmd"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/01RawData.zip.sha256"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/250211-Analysis.Rmd.sha256"
  },
  {
    "mediaType": "text/csv",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Brooks2015/AdditionalFile10.csv"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Brooks2015/AdditionalFile10.csv.sha256"
  },
  {
    "mediaType": "text/csv",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Brooks2015/AdditionalFile2.csv"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Brooks2015/AdditionalFile2.csv.sha256"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp1/16S/F_taxa_tab.txt"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp1/16S/F_taxa_tab.txt.sha256"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp1/WGS/taxa_tab.txt"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp1/WGS/taxa_tab.txt.sha256"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp2/16S/taxa_tab.txt"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp2/16S/taxa_tab.txt.sha256"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp2/WGS1/taxa_tab.txt"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp2/WGS1/taxa_tab.txt.sha256"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp2/WGS2/taxa_tab.txt"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3760/02DataAnalysis/Tabulated%20Data/Exp2/WGS2/taxa_tab.txt.sha256"
  }
]
identifier ark:/88434/mds2-3760
issued 2025-04-30
keyword 
[
  "Compositionality",
  "experimental design",
  "internal standard",
  "metagenomic sequencing",
  "scaled abundance"
]
language 
[
  "en"
]
license https://www.nist.gov/open/license
modified 2025-03-13 00:00:00
programCode 
[
  "006:045"
]
publisher 
{
  "name": "National Institute of Standards and Technology",
  "@type": "org:Organization"
}
theme 
[
  "Bioscience:Microbial measurements",
  "Mathematics and Statistics:Experiment design"
]
title A mathematical framework to correct for compositionality in microbiome datasets

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