Closed abspangler13 closed 1 year ago
abspangler13
commented
2 years ago Last round of this is still running. The output for this is confusing and bit unorganized so, feel free to contact me about what is what. It takes a long time to run so you probably don't want to have to do that again.
lcolladotor
commented
2 years ago Ok, thanks! I'll take a look next week and maybe talk about it with @lmweber too.
abspangler13
commented
2 years ago @lcolladotor my last run of nnSVG failed. I tried to log into JHPCE to look at the log files, but I think my access is gone. Just putting this here for your information.
lcolladotor
commented
2 years ago Thanks Abby!
lcolladotor
commented
1 year ago See https://jhu-genomics.slack.com/archives/C01EA7VDJNT/p1665090349917619 for more.
I think that we can get nnSVG to run by avoiding the for loop with an array job + reduce memory loads.
[x] ask tony about his code
[x] re-watch Lukas's talk from 6/30. https://jhu-genomics.slack.com/archives/CR9NYA0BF/p1656599274806249
[ ] use this to solved curvature of gyrus question. Find spatially variable genes of the just the two clusters around the curvature. Hypothesis is that this phenomenon is drive by a gene expressed in a gradient.
[x] meet w/ Lukas?
[x] do nnSVG for k = 16 all pairwise comparisons. only works for one sample at a time.
[x] run on specific pairs https://jhu-genomics.slack.com/archives/C01EA7VDJNT/p1658867952886359
[x] figure out why it's taking so much memory. Or submit jobs to multiple queues.
[ ] do just these pairs https://jhu-genomics.slack.com/archives/C01EA7VDJNT/p1659115769482389?thread_ts=1658429571.622209&cid=C01EA7VDJNT Pairwise: 5 vs. 9 (Layer 4?) Pairwise: 4 vs. 16 (Layer 5?) Pairwise: 7 vs. 13 (Layer "6A" vs. "6B") Pairwise: 12 vs. 13 (layer 6 apex vs Layer 6B Pairwise: 12 vs. 7 (layer 6 apex vs. layer 6A) Pairwise: 16 vs. 12 (layer 5 apex vs. layer 6 apex)
[x] combine pairs into one new cluster label, run nnSVG with new cluster label as covariate. Doing this for the first 3 pairs all together first since there are no overlapping cluster labels. The other ones will have to be done separately.