This repository contains scripts to generate the figures listed below for Yan et al. Cell Stem Cell 2018
*Mendeley Dataset 13 (http://dx.doi.org/10.17632/rd2sbgm35y.1) - TFvTO
*Figure 5C&D - Combat
*Figure 5B - TOvTFvFib
*Figure 4A and Mendeley Dataset 10 (http://dx.doi.org/10.17632/8v95h5rd6p.1) - SuperFreq
For Mendeley Dataset 13, Figure 5B,C and D. Execution of the R script will reproduce the core part of each of the respective Figure in the paper.
Fore Figure 4A and Mendeley Dataset 10, the SuperFreq directory only contains a template script and instructions to reproduce the figure as BAM and VCF files have to be first download from the EGA repository and scripts generated individually for each sample for execution on a high performance computer.