Benjamin Stewart

icon indicating an email [email protected]

icon location Cambridge, UK icon location Biomedical research: comp bio, single-cell genomics, nephrology.

Results 4 issues of Benjamin Stewart

anndata to seurat not working with scVI processed data

I have an anndata object which has been processed through the scVI pipeline. scVI adds `_scvi_extra_categorical_covs` and `_scvi_extra_continuous_covs` to obsm. These are dataframes not matrices. So SeuratDisk is throwing this...

input data normalisation

7 comment

Can you clarify what preprocessing is expected for the RNA assay (gene expression) data. Is the expected input integer (raw) counts or normalised&log transformed counts or similar? this isn't totally...

infer_grn errors

`infer_grn()` is giving me this error `Error in tf_g_cor[unique(tfs_use), , drop = F] : object of type 'S4' is not subsettable` is this the problem? ` tf_g_cor

reduced dimensions

would be useful to give an option to run on reduced dimensions that are not PCA For example 'X_scVI'