Tuomas Borman
Tuomas Borman
Hi, when there is NA in sample or feature names, the constructor throws an error which is hard to interpret. `Error in if (!ok) { : missing value where TRUE/FALSE...
HoloFoodR
Update the following URL to point to the GitHub repository of the package you wish to submit to _Bioconductor_ - Repository: https://github.com/EBI-Metagenomics/HoloFoodR Confirm the following by editing each check box...
Hello, @catiapacifico opened an issue to our framework that is utilizing SummarizedExperiment. https://github.com/microbiome/OMA/issues/202 This is quite rare case, but I thought that it is worth to let you know since...
1. Add exercise on how to use getTaxonomyLabels(). The exercise could be with import exercises. 2. In this exercise https://microbiome.github.io/OMA/docs/devel/pages/98_exercises.html#preliminary-exploration, the chapter number is incorrect. It should be 2.3 instead...
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....
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...
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...
We have 33 different branches which some might be deleted. We should probably remove those to keep repo clean
Hi, currently check contains NOTES. Especially it seems that syntax of list in roxygen has changed. 1. Run devtools::check() 2. List probelmatic things to this issue 3. Let's discuss what...
Currently, `addHierarchyTree` (`addTaxonomyTree`) replaces existing tree. Consider adding option for adding tree instead of replacing.