CCC Analysis of snRNA Data using LIANA

LieberInstitute / DLPFC_snRNAseq

snRNA_seq portion of the spatialDLPFC project

http://research.libd.org/spatialDLPFC/

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CCC Analysis of snRNA Data using LIANA #19

Closed boyiguo1 closed 1 year ago

boyiguo1 commented 1 year ago

CCC_toy.pdf

boyiguo1 commented 1 year ago

Set up job composer and run small-scale experiment (b2f36736b09cc5557744c6b88a33aa0b30d1f23b)

To analyze 1000 cells: LIANA uses less than 20 mins (range: 10-16 mins); Max vmem is 7 G

The two output file sizes are small too, on the MB scale. Screen Shot 2022-11-16 at 1 36 25 PM

boyiguo1 commented 1 year ago

The full-scale CCC is very fast: average 25 mins, max 30 mins. The memory required is smaller than imagined, Max 18G. Screen Shot 2022-11-16 at 2 29 57 PM

Nevertheless, there is a bug in the analysis that requires re-running the analysis (#20)

boyiguo1 commented 1 year ago

The results of each round of snRNA CCC move to #21

lcolladotor commented 1 year ago

Can we close this one @boyiguo1?