OMA
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microbiome
Orchestrating Microbiome Analysis
Nice paper about DAA methods https://arxiv.org/abs/2404.02691 Add citation to DAA chapter. Also, consider adding wrapper for wilcoxon text. 1. Relatively simple to implement for users also (basically just loop) 2....
I added this [citation](https://bioconductor.org/packages/release/bioc/html/BiocBook.html). For some reason, I have four commit but in reality only one file is changed.
After mia PR https://github.com/microbiome/mia/pull/536 that renamed the following function : - `subsampleCounts` --> `rarefyAssay` This PR replaces `subsampleCounts` with `rarefyAssay` in the OMA book.
The Multi-omics chapter has to be updated to use SE/TSE framework. See #394 and #437 for more details.
Mention in some suitable chapter that also mediation analysis is supported by mia. Or: exemplify the new mediation functionality in mia with a more detailed example. Avoid duplicating what is...
- Replace Hintikka link with https://microbiome.github.io/mia/reference/HintikkaXOData.html and add Tengeler link as https://microbiome.github.io/mia/reference/Tengeler2020.html (see chapter 2 for examplle) - explain the other mia datasets along with Hintikka and Tengeler which are...
Our new Nat. Medicine publication with Raes Lab [Tito et al. (2024)](https://www.nature.com/articles/s41591-024-02963-2) includes QMP profiling data and covariates of general interest (e.g. calprotectin, moisture). The species-level profiles are available as...
Standardize package names, functions and object types throughout OMA. one option is to use _italic_ for _R package names_, `monospaced` for `R functions (tse, assays, colData, altExp, phylo)` and simple...
Package import should be standardised across the book in a way that loads all packages at the bgining of the chapter. One method is to create `load_packages.R` file and source...
After mia PR https://github.com/microbiome/mia/pull/513 that renamed `splitByRanks` to `agglomerateByRanks` and added option `as.list` to specify whether the result of `splitByRanks` should be stored in alternative experiments, this PR replaces `splitByRanks`...