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scRNA-seq_simulation_Webvalley2020

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).

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