hanbin973 / fastrna_paper

Code for the FastRNA paper

FastRNA reproducible repository

Lee and Han (2022) currently under review at American Journal of Human Genetics

Contents

Code description

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.

Data availability

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.

Mouse embryo organogenesis data

Zhengmix8eq

PBMC SSC