The source code of RA3
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.
Requirements
- Matlab R2019a for the RA3 model
- Python 3.6.10 for the clustering
- R 3.6.1 for the visualization and downstream analyses
Usage instructions
-
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. 4a. -
plot_fig4_AMI_line.R: Fig. 4b and Supplementary Fig. 4b. -
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_umap.R: Supplementary Fig. 3. -
plot_GmHekInSiMCA.R: Supplementary Fig. 5. -
plot_dropout_cell_sum.R: Supplementary Fig. 6. -
plot_case_pbmc_all_other.R: Supplementary Fig. 7. -
plot_supp_diff_dim.R: Supplementary Fig. 8.
License
This project is built under license GNU GENERAL PUBLIC LICENSE (GPL).