Single cell RNA-seq and ATAC seq analysis of cardiac progenitor cell transition states and lineage settlement
This repository contains code and supplementary files for the analysis conducted in
Guangshuai Jia, Jens Preussner, Xi Chen, Stefan Guenther, Xuejun Yuan, Michail Yekelchyk, Carsten Kuenne, Mario Looso, Yonggang Zhou, Sarah Teichmann and Thomas Braun. Single cell RNA-seq and ATAC seq analysis of cardiac progenitor cell transition states and lineage settlement. Nature Communications 9, 4877 (2018), doi: 10.1038/s41467-018-07307-6.
Please cite the research article when using data from this repository.
The original analysis relied on the R programming languange and used R in version 3.5.0. Additionally, we heavily relied on the bioconductor package scater in version scater 1.4.0 for results from single-cell RNA-seq and scater 1.8.0 for results from single-cell ATAC-seq. The details on the session can be found in original-analysis/RNA-seq_sessionInfo.txt and original-analysis/ATAC-seq_sessionInfo.txt, respectively.
Please see the accompanying README.md for details on how to replicate preprocessing or re-create figures from the manuscript.
In addition to the original analysis, we will provide an up-to-date re-analysis of the data from the manuscript. Watch this repository to be notified on further updates.