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plger / scDblFinder

Methods for detecting doublets in single-cell sequencing data
https://plger.github.io/scDblFinder/
GNU General Public License v3.0
153 stars 18 forks source link

Compatibility between Seurat, matrix and scDblFinder versions #94

Closed hennion closed 7 months ago

hennion commented 8 months ago

We're trying to use scDblFinder in a environment with Seurat 5.0.1. It requires matrix > 1.6-2 which seems to be incompatible with scDblFinder. Is it possible to upgrade scDblFinder to make it compatible with recent versions of matrix and Seurat?

Thank you very much.

plger commented 8 months ago

Hi, There is no incompatibility per say, the problem is strictly with the pre-built binaries of Matrix and some packages on which scDblFinder depends -- see e.g. this comment and link in it. The solution, using the package versions or your liking, is simply to build those underlying packages locally, rather than using the pre-built binaries. You should be able to do this simply by specifying the type="source" argument when installing. I think this is only the irlba package but I'm not entirely sure, please let me know.

Tripfantasy commented 7 months ago

I think this is only the irlba package but I'm not entirely sure, please let me know.

In my case it was only the irlba package. This solution works great, thank you!

bestbakerpro commented 7 months ago

@plger I also met this problem，and I rebuilt irlba package. Now scDblFinder has worked great. install.packages("irlba",type = "source") Thank you！

hennion commented 7 months ago

It finally worked restarting from a clean environment and installing irlba from source. Thank you all for your help!