Ethan Weinberger
Ethan Weinberger
(Addresses #2393) While certain multimodal models (e.g. totalVI) can be used with either `AnnData` or `MuData` objects, currently the `ArchesMixin` class only supports `AnnData`-based models and so reference mapping cannot...
In the current (1.0.4) version of scvi-tools, multimodal models (e.g. totalVI) can be set up and trained with either AnnData or MuData objects. Thus, it would be nice to be...
Hi Jian, First of all, thanks for the awesome tool! I (along with @symoon) been investigating using SpaGCN for one of our projects. We're successfully able to reproduce the results...
Current MuData-based models save their `var_names` as a single list, with no information on which feature came from which modality. This is problematic for certain downstream features (e.g. reference mapping...
When splitting datasets into train/validation/test sets, I would expect that the union of train/validation/test samples should be equal to the full dataset. Moreover, data points should only be present once...
This PR adds a Jupyter notebook to download the data from McFarland et al., 2020 used to produce Figure 1 (i.e., response to idasanutlin and control DMSO for different cell...
This PR implements methylation variational inference (methylVI) for modeling methylation data from single-cell bisulfite sequencing (scBS-seq) experiments, described originally in [Weinberger and Lee (2024).](https://openreview.net/forum?id=Mg2DM0F3AY). In short, methylVI assumes that counts...