Daniel Dimitrov
Daniel Dimitrov
Hi @slobentanzer @nilskre, I have a couple of points wrt SQLLITE3 output adapter, and I wanted to hear your opinion on it. Currently the output is not exactly standard and...
- Add a tutorial on GPU-accelerated misty - Plot the weighted views, currently stored in .obsm and .var of each extra view
- pass `sample_key` explicitly - Make sure e.g. `samples_per_view` is a visible as a QC metric, and reduce it? - mention th `keep_stats` parameter - be explicit about `resource_name`
I should enforce a version for AnnData in the following updates w.r.t.: ```FutureWarning: The dtype argument is deprecated and will be removed in late 2024.```
Given how flexible and parameterized liana+ is, I should create a flow chart for the standard set of analyses.
LIANA+ supports MuData as input, hence with appropriate data transformation and resource; any multi-omics dataset can be used. To highlight this, I should include a tutorial on multi-omics data -...
The vignettes are starting to get many, and very large. They should be moved to another repository.
`liana.pl` currently relies on plotnine. While I chose this library due to how convenient it is to generate plots (and consistency with ggplot2), it's incompatibility with matplotlib is a drawback....
I should update the MOFAcell tutorial: - [ ] Cite published paper - [ ] Application with `df_to_lr` - [ ] Extend with functional analyses etc