Welcome to the GitHub page associated with Ting Zhao#, Yao Fu#, Jialiang Zhu#, Yifang Liu#, Qian Zhang#, Zexuan Yi#, Shi Chen, Zhonggang Jiao, Xiaochan Xu, Junquan Xu, Shuguang Duo, Yun Bai, Chao Tang, Cheng Li*, and Hongkui Deng*. "Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming." Cell Stem Cell 23 (2018): 1-15. Single-cell RNA sequencing analysis of chemical reprogramming depicts its trajectory and highlights dynamic intermediate cellular programs resembling early embryonic signatures. Zhao et al. apply these insights to develop a faster reprogramming system.
Most of the code following the tutorial from http://cole-trapnell-lab.github.io/monocle-release/docs/ and https://github.com/aertslab/SCENIC. So I recommend readers run the code from these tutorials first to be familiar with the single cell RNA-seq analysis pipeline.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114952
Please download GSE114952_AGG.tar.gz, unzip it and use it as raw data.
Questions and comments on this code can be e-mailed to liuyifang3000@gmail.com or create new issue.