Sam Wolock

Hi @TheSallyGardens, I haven't worked with scATAC-seq data and am not very familiar with the standard approaches for its analysis. I think that Scrublet's basic strategy could be used to...

Hi @ishwarvh, based on the error you're getting, I'm guessing `scrublet` hasn't been installed correctly. Can you tell me how you set it up on your system?

Sorry you're having so much trouble with this, but I haven't seen this problem before and do not know how to address it. I typically use miniconda to manage my...

Hi @hamishking, Assuming your Scrublet object is called `scrub` (as in the example notebooks), the scores and doublet predictions (True/False mask) are stored in `scrub.doublet_scores_obs_` and `scrub.predicted_doublets_`, respectively. You have...

Also, I should add some more visible documentation, but in general you can find an object or function's docs using the `help` function. For example, `help(scr.Scrublet)` lists the various attributes...

Yes, the scores will exactly match the original rows (=barcodes) of the counts matrix supplied to Scrublet.

Hi @DanSchnell After running `scrub_doublets()`, the standard errors (and a bunch of other stuff) are stored in the attributes of the `Scrublet` object (e.g., `scrub.doublet_errors_obs_` for the errors for the...

Hi @fangling0913 I haven't seen this format before, and I don't know of an existing python function to read it. The following code should do the job, but be warned...

Hi @s849, apologies for the very delayed response. Your approach does sound correct to me. As an aside, the results shouldn't depend all that much on the input `expected_doublet_rate`, as...

Hi @danielcgingerich, have you managed to figure this out? It looks like `scrublet` might not have been installed properly... How did you install it?