DE analyses of scRNA-seq data with plate effects

To run the simulation and analysis code:

1. Download the count table from http://www.ebi.ac.uk/teichmann-srv/espresso, and store it in a (newly created) reference/ESpresso subdirectory.
2. Run reference/submitter.sh to construct a simulation function based on real data.
3. Run simulations/submitter.sh to perform the simulations for type I error control and power. This assumes you have an LSF system, otherwise remove the bsub preamble in front of each job to run it in a standard fashion. The make_*_images.R scripts are used to make plots of the simulation results.
4. Run realdata/submitter.sh to analyze the mESC data. Individual R scripts in realdata are also responsible for generating plots -- process_real.R to generate barplots, plottop_ESpresso.R for the top DE genes, and rank_ESpresso.R to get the top DE pluripotency factors.

The manuscript directory contains all the LaTeX source code for the manuscript. This can be compiled with make.

The extrasim directories contain other diagnostic scripts that were used to check the behaviour of certain methods.