Severin Dicks
Severin Dicks
This adds support for rapids-singlecell for the `over clustering` #110 . The results might differ a bit since rsc uses a brute-force knn approach and the leiden clustering is also...
Its really cool to see that @canergen already added in cuml support for the training. I would also like to add GPU support for the Majority voting part. Would this...
This adds dask support Functions to add: * [x] `calculate_qc_metrics` * [x] `normalize_total` * [x] `log1p` * [x] `highly_variable_genes` with `seurat` and `cell_ranger` * [x] `scale` * [x] `PCA` *...
Please don't use cuml-23.08 with cuda 12. PCA will fail for larger datasets https://github.com/rapidsai/cuml/issues/5555
Adds a numba kernel for `seurat_v3` for sparse matrices. This kernel is a lot faster and more memory efficient. I doesn't copy nor promotes the matrix to 64-bit floats.
With the new numba kernel for sparse scaling, we need to figure out how and when the numba code becomes faster than the array code. This might lead to numba...
**Describe the bug** The return value element of transform has no shape and cant be integrated into a existing data structure without calling PCA.compute_chuch_sizes() because its has no size. **Steps/Code...
This updates _pre for faster dataloading. I also changed `tqdm` to `tqdm.auto` so that it looks better in notebooks
Within `_pre.extract` you don't support `layer` and `use_raw` is set to true by default. I would suggest to add support with `_get_obs_rep` from scanpy (it's small codeblock that you can...