OMA
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microbiome
Orchestrating Microbiome Analysis
Right now[ Docker container](https://github.com/js2264/OMA/pkgs/container/OMA) is very basic and cannot be used. I managed to run in with [Podman](https://podman.io/) 4.8.3 : ```bash podman pull https://github.com/js2264/OMA/pkgs/container/OMA podman run --rm -p 8787:8787 ```...
Add an example showing how pairs of points can be connected on beta diversity map.
The addTaxonomyTree creates rowTree based on taxonomic rank hierarchy. This is different from the actual phylogenetic tree and may cause confusion. I suggest to remove addTaxonomyTree from examples entirely, or...
Consider structure of OMA. How much general information there should be about microbiome data science (not directly related to miaverse)? Should we structure the book differently? Currently it seems that...
This chapter should be carefully checked, there were various suboptimal choices.
Rearrange and improve the [outreach material](https://github.com/microbiome/outreach)
We should have some exercises about all major chapters / functionalities. List systematically what is missing and create issue/issues. At least: - dbRDA exercises will require an update - calculating...
Add link and explanation of [Microbiome Compendium](https://github.com/seandavi/MicroBioMap#microbiome-compendium) in OMA.
Google Colab would enable easy testing and trying for new-comers. There could be short example notebook that is implemented with Google Colab --> now local installation needed, just Google account...
RDA plots can indicate both features as well as covariates that influence ordination. Would be good to show examples in OMA, too. Here some examples: https://stackoverflow.com/questions/32194193/plotting-rda-vegan-in-ggplot Here some discussion on...