Artur Sannikov

It now works pretty well. With pre-cached builds, it takes a couple of minutes to build the dev environment with RStudio.

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.

Improve Docker container

14

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 ```...

Use a different MAE data for more meaningful MOFA results

1

**Is your feature request related to a problem? Please describe.** At the moment, Hintikka data is used for basically all analysis in OMA book. However, I see a problem in...

More layouts for plotAbundanceDensity

1

There are only three possible layouts for [plotAbundanceDensity](https://microbiome.github.io/miaViz/reference/plotAbundanceDensity.html) function. Resulting plots are often cluttered and not informative. More plot options can be added, for example boxplots that can measure counts...

Make create_mofa_from_MultiAssayExperiment() accept alternative experiments

8

**Is your feature request related to a problem? Please describe.** Currently, to use `create_mofa_from_MultiAssayExperiment()` on agglomerated data, we have to directly modify the original MAE assays. In contrast `getExperimentCrossAssociation()` is...

Use `pseudocount=TRUE` in `transformAssay` even with missing or zero values

9

**Is your feature request related to a problem? Please describe.** At the moment, `transformAssay` [function](https://github.com/microbiome/mia/blob/master/R/transformCounts.R#L556) requires specifying a numerical value manually if there are negative or missing values in the...

As of ggplot 3.3.4, I get this warning: ``` Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as of ggplot2 3.3.4. ℹ The deprecated feature was...

All blog posts lead to page 404. * [Make circular heatmaps](https://jokergoo.github.io/2020/05/21/make-circular-heatmaps/) * [Multiple-group Chord diagram](https://jokergoo.github.io/2020/06/08/multiple-group-chord-diagram/) * [Changes in circlize 0.4.10](https://jokergoo.github.io/2020/06/14/changes-in-circlize-0.4.10/) * [x-axes in the circular plot](https://jokergoo.github.io/2020/08/17/reverse-x-axes-in-the-circular-plot/)

Hardcoded row selection in Multi-omics Integration chapter

1

Currently, the selection of rows for Intermediate Fusion algorithm is [hardcoded](https://github.com/microbiome/OMA/blob/devel/inst/pages/IntegratedLearner.qmd#L360). A better solution would be to select indices based on FeatureType. ```R pathways_ind