Ben Parks

Hi @aarebeca, thanks for your question! You can definitely use BPCells to analyze the scRNA-seq portion of your data and combine those results for plotting with any values or metadata...

Hi @Zilong-Li, thanks for reaching out! Your paper and R package seem like an interesting SVD method. I've previously had success implementing randomized SVD from Halko Algs 4.4 and 5.1...

Hi @Zilong-Li, I haven't seen an email arrive from you -- if you sent one maybe there was an email address mixup? I've been busy finalizing the BPCells preprint, but...

Hi Rebeca, Overall, yes this is possible but it is a bit tricky since Seurat has not fully updated their SCTransform functions to work with BPCells objects. I'll put some...

Hi @yxsee, currently BPCells can support regressing out variables via a linear regression model with [`BPCells::regress_out()`](https://bnprks.github.io/BPCells/reference/regress_out.html), but it does not currently support regressing out variables via a negative binomial GLM...

That sounds like a reasonable use-case. I'll see if we can put on our development to-do list to update our SCT implementation to support regressing out variables like this. I...

Nice initiative on putting in a suggested fix, but I think the equation rendering is fixed already by a pending change that's currently in PR 189, as described in my...

Hi Aaron, thanks for your question! There's not a built-in function to do this right now in BPCells, but it's possible to calculate by combining the existing supported operations. I've...

Hi @kollo97, thanks for following up with some more detail and benchmarking. The solution I suggested to you obviously performs quite poorly on your mini benchmark, and it looks like...

Hi @kollo97, we've been a little slow getting this reviewed and merged, but the code is available in PR #243. I believe if you want to install a test version,...