The source code for the reproduction of results in "A reference-guided approach for epigenetic characterization of single cells".
We also provide a R-based implementation for the convenience of the community.
- Matlab R2019a for the RA3 model
- Python 3.6.10 for cell clustering
- R 3.6.1 for data visualization and downstream analyses
Code | Function |
---|---|
RA3_func.m |
main function of RA3 model |
RA3_script.m |
data preprocessing and model initialization of RA3 |
run_RA3_script.m |
running script of RA3 |
plot_case_fig1.R |
Fig. 1bcef |
plot_residual.R |
Fig. 1d |
plot_case.R |
Fig. 2abc, Supplementary Fig. 1bcde, and Supplementary Fig. 2abdef |
plot_case_pbmc.R |
Fig. 2d and Supplementary Fig. 2cg |
plot_fig3_scatter.R |
Fig. 3 |
run_clustering_RA3.py |
clustering of RA3 |
plot_fig3-2_AMI_bar.R |
Fig. 4a and Supplementary Fig. 6a |
plot_fig4_AMI_line.R |
Fig. 4b and Supplementary Fig. 6b |
plot_bar_ragi.R |
Fig. 4c |
trajectory.R |
trajectory inference, Fig. 5a |
cluster_specific_peak.R |
cluster specific peaks |
chromVAR_motif.R |
motif analysis, Fig. 5b |
plot_corr3.m |
Supplementary Fig. 1a |
plot_scatter_prop.R |
Supplementary Fig. 3 |
plot_bar_prop.R |
Supplementary Fig. 3 |
plot_LOpeak.R |
Supplementary Fig. 4 |
call_peak_iter |
pipeline for iterative peak calling |
plot_umap.R |
Supplementary Fig. 5 |
plot_GmHekInSiMCA.R |
Supplementary Fig. 7 |
plot_dropout_cell_sum.R |
Supplementary Fig. 8 |
plot_case_pbmc_all_other.R |
Supplementary Fig. 9 |
plot_clusterTable.py |
Supplementary Fig. 10 |
plot_time_bar.R |
Supplementary Fig. 11 |
plot_tfidf_scatter.R |
Supplementary Fig. 12 |
plot_tfidf_bar.R |
Supplementary Fig. 12 |
plot_scatter_tau0.R |
Supplementary Fig. 13 |
plot_scatter_tau1.R |
Supplementary Fig. 13 |
plot_scatter_theta.R |
Supplementary Fig. 13 |
plot_scatter_K2.R |
Supplementary Fig. 13 |
plot_scatter_K3.R |
Supplementary Fig. 13 |
plot_scatter_tau0_LObulk.R |
Supplementary Fig. 14 |
plot_scatter_tau1_LObulk.R |
Supplementary Fig. 14 |
plot_scatter_theta_LObulk.R |
Supplementary Fig. 14 |
plot_scatter_K2_LObulk.R |
Supplementary Fig. 14 |
plot_scatter_K3_LObulk.R |
Supplementary Fig. 14 |
plot_scatter_refPC.R |
Supplementary Fig. 15 |
This project is built under license GNU GENERAL PUBLIC LICENSE (GPL).