Lee and Han (2022) currently under review at American Journal of Human Genetics
The codes for running R code are in the fastrna_r folder.
The codes for running python code are in the fastrna_py folder.
Data can be downloaded following the instruction in the manuscript's Materials and Methods.
Figure 1 can be produced using *-mouse-organogenesis.ipynb.
Figure 2 can be produced using *-zhengmix8eq.ipynb.
Figure 3 can be produced using *-pbmcssc.ipynb.
Figure 4 can be produced using *-mouse-organogenesis.ipynb and *-splatter-*.ipynb.
For all datasets, the matrix files were converted to numpy sparse file format .npz.
It was because the .npz format was the fastest to load into memory especially for the mouse embryo organogenesis dataset which was large in size.