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CCBR / reneeTools

R helper functions for RENEE
https://ccbr.github.io/reneeTools/
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investigate how S7 object size increases #37

Closed kelly-sovacool closed 2 hours ago

kelly-sovacool commented 2 months ago

as we add raw, filtered, normalized counts, how does the memory usage of the object increase?

kelly-sovacool commented 1 month ago

step up from 10, 50, 200, to 500 samples. ~58,000 genes.

store raw, filtered, and normalized counts.

make pretty plots showing how object memory size increases with increasing samples.

kelly-sovacool commented 1 month ago

Also compare to average Seurat object (can't be the same dataset as for reneeTools, seurat is for single cell). This should take an order of magnitude less.

kelly-sovacool commented 3 weeks ago

pryr::object_size() https://rdpeng.github.io/RProgDA/the-role-of-physical-memory.html

kelly-sovacool commented 2 weeks ago

image

kelly-sovacool commented 3 days ago

now with comparison to seurat (single cell) objects

image image

kelly-sovacool commented 2 hours ago

completed

source code for plots: https://github.com/CCBR/reneeTools/blob/7773ad0530d82871b0573c7fc87f0c48842d389a/vignettes/memory.Rmd