A Sensitivity Analysis of Methodological Variables Associated with Microbiome Measurements
This repository provides the raw data, analysis code, and results generated during a systematic evaluation of the impact of selected experimental protocol choices on the metagenomic sequencing analysis of microbiome samples. Briefly, a full factorial experimental design was implemented varying biological sample (n=5), operator (n=2), lot (n=2), extraction kit (n=2), 16S variable region (n=2), and reference database (n=3), and the main effects were calculated and compared between parameters (bias effects) and samples (real biological differences). A full description of the effort is provided in the associated publication.
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, analysis code, and results generated during a systematic evaluation of the impact of selected experimental protocol choices on the metagenomic sequencing analysis of microbiome samples. Briefly, a full factorial experimental design was implemented varying biological sample (n=5), operator (n=2), lot (n=2), extraction kit (n=2), 16S variable region (n=2), and reference database (n=3), and the main effects were calculated and compared between parameters (bias effects) and samples (real biological differences). A full description of the effort is provided in the associated publication. |
| distribution |
[
{
"title": "resources",
"format": "R markdown document.",
"mediaType": "application/zip",
"description": "R code for analysis and figure generation.",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/resources.zip"
},
{
"title": "00README",
"mediaType": "application/rtf",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/00README.rtf"
},
{
"title": "DataAnalysis",
"mediaType": "application/octet-stream",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/DataAnalysis.Rmd"
},
{
"title": "ProcessingRawReads",
"mediaType": "application/octet-stream",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/ProcessingRawReads.Rmd"
},
{
"title": "dada2_output/v3_taxa_tab3Silvav132",
"mediaType": "text/plain",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv3_taxa_tab3Silvav132.txt"
},
{
"title": "dada2_output/v3_taxa_tab3Silvav138",
"mediaType": "text/plain",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv3_taxa_tab3Silvav138.txt"
},
{
"title": "dada2_output/v3_taxa_tab3rdp18",
"mediaType": "text/plain",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv3_taxa_tab3rdp18.txt"
},
{
"title": "dada2_output/v4_taxa_tab3Silvav132",
"mediaType": "text/plain",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv4_taxa_tab3Silvav132.txt"
},
{
"title": "dada2_output/v4_taxa_tab3Silvav138",
"mediaType": "text/plain",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv4_taxa_tab3Silvav138.txt"
},
{
"title": "dada2_output/v4_taxa_tab3rdp18",
"mediaType": "text/plain",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv4_taxa_tab3rdp18.txt"
},
{
"title": "raw_reads",
"mediaType": "application/zip",
"downloadURL": "https://data.nist.gov/od/ds/mds2-3092/raw_reads.zip"
}
]
|
| identifier | ark:/88434/mds2-3092 |
| issued | 2023-11-16 |
| keyword |
[
"design of experiments",
"full factorial",
"metagenomic sequencing",
"microbiome"
]
|
| landingPage | https://data.nist.gov/od/id/mds2-3092 |
| language |
[
"en"
]
|
| license | https://www.nist.gov/open/license |
| modified | 2023-10-05 00:00:00 |
| programCode |
[
"006:045"
]
|
| publisher |
{
"name": "National Institute of Standards and Technology",
"@type": "org:Organization"
}
|
| theme |
[
"Bioscience:Microbial measurements"
]
|
| title | A Sensitivity Analysis of Methodological Variables Associated with Microbiome Measurements |
