Tuomas Borman
Tuomas Borman
[The ordination method section](https://microbiome.github.io/OMA/docs/devel/pages/20_beta_diversity.html#sec-unsupervised-ordination) does only describe available methods, but does not really say the difference between them, and when to use them. (the differences in interpretation) - The UMAP...
Seems good! Title options: - Orchestrating microbiome analysis - Orchestrating microbiome data science - Orchestrating microbiome analysis with Bioconductor - Orchestrating microbiome data science with Bioconductor Data science might be...
iSEEtree and miaSim examples are missing from the book. At least, they should be mentioned.
https://github.com/microbiome/OMA/pull/562 All packages should be in format \`package\`, all functions should be in format \`function()\` and all slots should be in format \`assay\`. Now the book contains multiple different styles....
https://github.com/microbiome/OMA/pull/562 RDA example is outdated. It asks reader to use vegan functions, even though we have easy wrapper for RDA: addRDA(). Modify the exercise so that user is asked to...
https://github.com/vegandevs/vegan/blob/69de595e4f47918ab7f893e9578647983cc3b3c5/R/decostand.R#L149 Hi, I noticed that `na.rm` is not used in CLR calculation. -Tuomas
When SingleCellExperiment is converted into SummarizedExperiment, the resulting SE does not include rowData that was in the input, ``` library(SingleCellExperiment) # Create dummy data n_cells
Hello, some of the examples in OMA are too complex. The examples should be clear enough without unnecessary complexity because it might a) prevent readers to get interested on the...
Hello, this PR is partly overlapping with this one: https://github.com/microbiome/mia/pull/637 I completely rewrote *RDA and *CCA functions. That is for easier maintenance and to make the code simpler. I have...