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TuomasBorman
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TuomasBorman
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Thansk! Sorry I have been very busy lately. Going through these PRs now...
| ### Integrative human microbiome project | ||
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| Datasets from the second phase of the human microbiome project, also known as | ||
| integrative human microbiome project are made available with `r BiocStyle::Biocpkg("HMP2Data")`[@HMP2data]. | ||
| The datasets are offered as `TreeSE` objects. Additional data, *e.g.* cytokines, | ||
| is included when available. | ||
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| ### Microbiome benchmark data | ||
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| The `r BiocStyle::Biocpkg("MicrobiomeBenchmarkData")` allows access to datasets | ||
| with some groundtruth available[@Gamboa-Tuz2025]. These datasets are compiled for the purpose of | ||
| benchmarking differential abundance methods, but the ground truth may be useful | ||
| for other benchmarking applications. Datasets are offered directily as `TreeSE` | ||
| objects. |
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Can you add them also here: https://microbiome.github.io/OMA/docs/devel/pages/miaverse.html#sec-sub-diff-abund
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Btw, you could try to make the table more pretty. The idea of that table is to list all packages that have TreeSE support.
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Let us also avoid duplication i.e. document external data sets in a single place, and cite that section from elsewhere as relevant?
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In addition, we can link curatedMeagenomicData3 (https://www.nature.com/articles/s41467-025-66888-1). We also suggested adding HoloFoodR package to OMA (EBI-Metagenomics/HoloFoodR#9). It provides simple access to a lot of data in TreeSummarizedExperiment and MultiAssayExperiment data containers. |
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@raivo-otus Any updates on this? |
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Add section and references to a few more open data resources with TSE support.
Resolves #816