Andrew Chen

Parameters relevant for speed in mutate_mol

11

Hi! Thanks for maintaining this repo! I was wondering which parameters were relevant for speeding up `mutate_mol`? I've found better speeds by increasing `n_cores` but if I wanted to speed...

Batch-Corrected Counts from RPCA with log-normalized counts

1

Similar question to the one raised in [8146](https://github.com/satijalab/seurat/issues/8146) but for log normalized data. But running integration with `IntegrateLayers` as demonstrated in the [vignette](https://satijalab.org/seurat/articles/seurat5_integration), doesn't return a batch-corrected counts layer if...

Adding Seurat's RPCA method to Benchmarking tasks?

3

Hello! I noticed that Seurat's RPCA integration method was not included in either the '[Batch integration embed](https://openproblems.bio/results/batch_integration_embed/)' task or the '[Batch integration feature](https://openproblems.bio/results/batch_integration_feature/)' task. I know that RPCA is capable...

Multiple covariates use case

1

Hello authors of sccomp! Not a bug here, but just wondering what the correct way to specify this regression is. I'm trying to regress cell type abundance (as specified by...

Hello! Noticed that the AUCell scores change depending on the number of genesets tested. I'm using the toy data below and the values are the different: cells_AUC_1: ``` AUC for...

Hello! Thanks for releasing this package! I was wondering if there was the capability of adding prior edges/or enforcing forbidden edges in the structure learning step? Thanks!