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microbiome
Orchestrating Microbiome Analysis
Ref: Pat Schloss' [recent analyses](https://www.biorxiv.org/content/10.1101/2023.06.23.546313v1.full.pdf) on rarefaction in alpha & beta diversity. This addressess well some of the long debates and controversies surrounding rarefaction in microbial ecology. Based on this...
See #394 - @YihanLiu4023 could you have a brief look at this one?
Hi! Currently, the [visualisation chapter](https://microbiome.github.io/OMA/docs/devel/pages/19_visualization_techniques.html#heatmaps) shows heatmap examples with multiple packages (pheatmap, sechm and ggplot). These examples require a great deal of manual manipulation of the generated graphics to resize...
ANCOMBC package supports TreeSE and contains [new SECOM method for co-occurrences](nature.com/articles/s41467-022-32243-x). Consider adding an example.
The MOFA Bioc package (see https://microbiome.github.io/OMA/multi-assay-analyses.html) requires a bit multi-faceted process for MAE data -> assess whether we could support PR or wrapper to enable MAE support for the MOFA...
It seems we have overlapping content on adonis/dbrda calculations in sections 7.3.1 and 7.2. The former uses vegan and base R, the latter uses mia & runRDA. I suggest to...
Moving here [miaViz issue #40](https://github.com/microbiome/miaViz/issues/40) Row/col sorting based on angle on MDS projection is implemented in SEtools R package. The [vignette](https://www.bioconductor.org/packages/release/bioc/vignettes/SEtools/inst/doc/SEtools.html) says "By default, rows are sorted not with hierarchical...
This was feedback from a course. Good idea. Another option is to publish workflows as separate worfklow publications (e.g. F1000 Bioc pathway) and link to them from OMA. OSCA has...
The exercises in 17.5 and perhaps also other parts in OMA could indicate more clearly from which package functions come from, e.g. plotColData is scater::plotColData
We have used this recently in e.g. [Ruuskanen et al.](https://www.tandfonline.com/doi/full/10.1080/19490976.2021.1888673). Cite the original phILR paper and this one at least for references. Complements CLR transformation, and utilizes phylotree.