This repository contains the Jupyter notebooks about the simulation of single cell RNA-seq count data using SPARSim.
The official guide of SPARSim (sparsim_vignette.html) and the slides (Simulation_SingleCell.pdf) are also avaible in the repository.
The description about the simulation scenarios described by each notebook is available in the slides.
Some important notes:
- Example 4 and Example 5 may require a considerable amount of resources (up to 8GB of RAM) and require several minutes of computation
- The documentation about SPARSim functions and parameter presets is available typing
?<function name>(e.g.?SPARSim_simulation) or?<presets_name>(e.g.?Zheng_param_preset) inside a R shell. - The official guide of SPARSim is available also typing
browseVignettes("SPARSim")inside an R shell (it doesn't work in R shell from JypyterLab).