scrublet

scrublet copied to clipboard

input data with pearson residuals workflow

2

Hi, nice work! If I would to use [pearson residuals ](https://scanpy.readthedocs.io/en/stable/generated/scanpy.experimental.pp.highly_variable_genes.html)to normalize and find hvgs, I'm wondering when use other external apis such as scrublet. currently in the [doc](https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.scrublet.html): >...

brainfo

Hello I would like to know if there is a way to generate scrublet output file with the respective cell barcodes? that will be helpful to add output data to...

azwainCC

Hello I am seeing the number of genes list in my sample with scrublet functions below is different(23932) from that I see in Seurat files (17229) which is not allowing...

IlianCx

Kernel died when running scrublet

2

Hi, thanks for your powerful tool. I got kernel died error when I run codes as tutorials from scenic+. ``` doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=3, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=30) Preprocessing... Simulating doublets......

UboCA

fit_percentile parameter of function get_vscores has default value 0.1. It is then passed to np.percentile through runningquantile function. So 0.1 percentile, that is 0.001 quantile is used. That looks unreasonably...

iaaka


ouyangcuihuaa

Do I use scrublet after doing the standard preprocessing from Seurat?

1

I am trying to figure out at which point I should use scrublet. Am I supposed to do it after doing the standard preprocessing from Seurat and then import the...

st4302

Rolling back uninstall of llvmlite

2

I was trying to install scrublet but got stuck at the last step: ``` ~/tools/scrublet$ sudo pip3 install --upgrade . Running setup.py install for pillow ... done Found existing installation:...

brianpenghe

pip install error

2

Hello, We are trying to install scrublet using pip but we get the error below. Could you please provide guidance on how to deal with this? Thanks! -------------------------------------------------------------- Processing /user/scrublet...

ulloaa

How to delete doublets from Seurat object

1

Hello I have worked upto generating doublet score tsv files through scrublet. however I am having difficulty in adding these files to the metadata of Seurat object and further deletion...

GreyRockIQ