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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
297 stars 54 forks source link

Cellbender v.0.3.0 not working with Seurat Read10X_h5 function #315

Open smk5g5 opened 11 months ago

smk5g5 commented 11 months ago

Hi,

I am using the output from Cellbender v.0.3.0 '*_filtered.h5' file. Whenever I try to load it using Seurat's Read10X_h5 I get the following error. It would help if you can explain why that is so. In the past whenever I have used Cellbender output with Seurat I never had this problem. I would appreciate if you can enlighten me on how to make it work. Thank you!

z5ouyang commented 11 months ago

https://cellbender.readthedocs.io/en/latest/tutorial/index.html#open-in-seurat

OneHitKO commented 5 months ago

In case other people are wondering, there's a very convenient Read_CellBender_h5_Mat() wrapper from {scCustomize} (https://samuel-marsh.github.io/scCustomize/)!

JZL commented 4 months ago

Every time and always @samuel-marsh 's scCustomize comes in handy. I highly recommend it!