Lisa Sikkema

feature request: split screen option

6

Hi! I'm working a lot with cellxgene and one thing that would be really useful for me is a split-screen option, allowing for two UMAPS colored in two different ways....

Hi, I'm working on a very large integration of many datasets, and me and my collaborators use cellxgene to explore the data. One thing we would really like, is the...

Hi, I am working with MNN, and was wondering why in the paper sometimes the union of the highly variable genes (HVGs, calculated within batches) is used, whereas other times...

batch and max_kl_weight parameters ignored when mapping to scvi reference

7

Hi! I have been trying to map data to scvi-integrated embeddings using scArches, and have noticed that for the two scVI-based reference models I have used, setting the `max_kl_weight` parameter...

Label transfer code producing different outputs in different environments

10

Hi, As discussed with @alextopalova and @M0hammadL , the label transfer code that you guys recently added to the scArches code base produces different output depending on (I think) the...

Suggested improvements for label transfer function

1

Hi @M0hammadL @alextopalova , Here are some of my comments on/suggestions for your label transfer code: 1. Could it be that this code is not yet part of the pip-installable...

Hi! It would be really great if you could somehow make the function `sca.models.SCANVI.prepare_query_anndata` able to take into consideration both gene Ensembl IDs and gene symbols (i.e. actual gene names),...