the remove-background data named output.h5 has 0 genes.

broadinstitute / CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

https://cellbender.rtfd.io

BSD 3-Clause "New" or "Revised" License

280 stars 50 forks source link

Open Tycooner opened 8 months ago

Tycooner commented 8 months ago

when I get the remove-background data named output.h5, i found there is no genes in the data!!! why?

KarlKaise commented 6 months ago

I have same issue. Would be grateful for any help

yuanjianwen-gif commented 4 weeks ago

I got same problem, any solution?

yuanjianwen-gif commented 4 weeks ago

from cellbender.remove_background.downstream import anndata_from_h5

adata = anndata_from_h5('output.h5') adata

yuanjianwen-gif commented 2 weeks ago

sc.read_10x_h5("filter_filtered.h5", gex_only=False) also work for me