Daniel C. Jones
Daniel C. Jones
I need to update the documentation, but you shouldn't need to deal with `stitch-cosmx.jl` anymore. Previously they were not generating these flat files, so I had to figure out how...
It seems xeniumranger 3 introduced some incompatibilities. I just released proseg 1.1.6 which should fix these issues. Thanks for reporting!
My recommendation is to use expected counts if you can. Because proseg is a sampler, this is essentially what it natively computes (that is, parameters averaged over multiple samples). The...
Hmm, I have some ideas but it's hard to know for sure. I'll see if I can find a dataset I can reproduce this on. This may be too much...
Sure, this is something I should document, but there are a bunch of command line arguments that will sometimes let proseg interpret a format it doesn't officially support if it...
This is expected. Since visium data is encoded in a sparse matrix, not a transcript table, it includes every gene in the gene panel or index, even if if that...
Hi Lauritz, I have seen this error occasionally, but usually when something has gone wrong with the input (or proseg's interpretation of the input). For example, if the prior segmentation...
Yeah this is pretty interesting. Now that protein data is available, some measure of the agreement between RNA and protein before and after trying to correct for diffusion could be...
This looks interesting, thanks for the link!
You will get examples like this, but my hope is that they are relatively rare and that most disconnected cells are trivially so like this: The other thing that complicates...