Ben Parks

I've been able to reproduce this on a Mac and have made a few observations: - Using the homebrew hdf5 library on MacOS hits the crash - Using the BPCells...

I noticed that git messes with the CRLF endings by default which makes the test files a bit tricky to preserve line endings on. I added additional checks in the...

Hi @sbt2024, thanks for your question. With normal Seurat conventions, accessing the data layer as you do would return log-normalized data, not raw counts. If you want raw counts, the...

Yes, `as(bpcells_mat, "dgCMatrix")` should work as expected whether you have counts, log-normalized data, or any other set of transformations on the matrix. You can mostly think of BPCells matrix objects...

EDIT: oops, didn't spot that the LSI code had all been collapsed in the diff view. Will update below in a bit I'm assuming this is still in-progress since the...

Hi @Baboon61, thanks for your question and other issue reports -- it's very helpful to get user feedback. In general, BPCells and ArchR should produce the same results for gene...

Hi @Baboon61, apologies for not noticing your reply promptly. When ArchR encounters nested genes, it computes the extensions very strangely. If we look at the nested genes SYN2 and TIMP4...

Thanks for this update, very clearly written Discussion points: - New idea for the base name, maybe `select_features_[method]` instead of `variable_features_[method]`? I think this might side-step some confusion that some...

I was originally thinking clustering + pseudobulk calculation could happen in iterative_lsi. Then we still have a parameter in iterative_lsi to let the user configure how feature selection happens (which...

Hi @ycli1995, thanks for the PR! It might be a week or two before we can fully process this, but just letting you know I've seen the PR and I'll...