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Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
ohih8
changed the title
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Note: this PR included both new protocols, which is why I deleted the old PR with just one of them. |
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When PRs are related to an issue, include in the Description something like "Closes #n" so that merging the PR will automatically close the issue, and both will cross-reference each other. If not relating to an existing issue, file an issue so you can reference it in the PR. |
| license: CC-BY-4.0 | ||
| type: atomic | ||
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| protocol_citation: "10.1038/s41467-025-66888-1" |
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Cite original research for something this commonly used
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| # Microbiome Diversity Analysis | ||
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| This protocol calculates one within-sample diversity value (alpha diversity) for |
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Separate alpha diversity protocol from beta-diversity protocol
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| ### Step 1: Define the analysis set and analysis objectives | ||
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| Specify the body site, participant population, study-design restrictions, repeated |
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I don't think body site affects how the calculation is performed, and it is not part of the Materials.
| ### Step 1: Define the analysis set and analysis objectives | ||
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| Specify the body site, participant population, study-design restrictions, repeated | ||
| sample rule, and exclusion criteria before calculating diversity. Retain a record of |
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I think all this is separate, alpha diversity should just be calculated on an input matrix
| every excluded sample and the reason for exclusion. Do not select samples based on | ||
| their diversity values or on a result of the group comparison. | ||
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| State which outputs are required: alpha diversity, beta diversity, alpha-diversity |
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Inputs should be part of Materials, and could include which measure of alpha or beta diversity is to be calculated
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| ### Step 1: Confirm the input abundance scale and taxonomic identifiers | ||
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| Use species-level relative abundances for both the oral reference samples and the gut |
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| Require every abundance used in the calculation to be numeric, finite, and | ||
| non-negative. Treat an explicit numeric zero as zero. Do not treat a missing value, | ||
| blank value, or non-numeric value as zero; resolve it or stop the calculation. |
| different species; stop and report any unresolved identifiers that could affect the | ||
| oral signature or its gut-sample abundances. | ||
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| ### Step 2: Select oral-cavity reference samples |
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| The original study used 857 oral-cavity samples from curatedMetagenomicData 3. A | ||
| different reference collection may be used, but its source, body-site definition, | ||
| sample count, and study composition must be recorded because they determine the |
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Try to compress without loss of precision
2 participants
Calculate within-sample and between-sample microbiome diversity and test whether diversity differs by a prespecified grouping variable.