Maren Büttner
Maren Büttner
- [ ] Additional function parameters / changed functionality / changed defaults? Hi there, it would be great to have the counts layer being added automatically to the anndata object...
Hi there, I have been trying to implement an MLP to predict cell type labels using pyTorch Lightning and the AnnLoader function. For the implementation, I followed the [AnnLoader tutorial...
kBET is slow and partly because it's running many computations multiple times (for instance, to obtain good stats for the rejection rate). - [ ] ensure that neighbourhoods are computed...
kBET requires a dense matrix as input, even if kBET will only use a knn graph. - [ ] Include sparse matrix computation - [ ] Remove requirement of data...
kBET uses the entire data matrix currently, and when kBET needs to be computed per cell type, one has to subset per cell type manually. kBET should handle this internally...
I wrote this adjustment for Combat for a recent publication (Boettcher et al, 2020): https://www.biorxiv.org/content/10.1101/2020.08.12.247585v1 It allows to compute a ComBat for control cells and apply this to a second...
This PR provides a fix to the issue stated in https://github.com/aertslab/scenicplus/issues/61. How it's done: Scaffold chromosomes are filtered out in the `export_pseudobulk` function when the fragments are loaded as DataFrame...
### PyPI Username maren.buettner ### Reason for request Primary email address has been deactivated. Secondary email address could be verified. ### Code of Conduct - [X] I agree to follow...
Hi there, I wrote a color annotation function for the Baseplot class called `add_colorblocks()`, which borrows some functionality of the `add_totals()` function and creates a colorblock for the annotation each...
I worked on the function `counts_fragments_features` to count fragments in arbitrary peak annotations and found a few issues when working with pysam. It is working for my data now, but...