/RA3_source

The source code for the reproduction of results in "A reference-guided approach for epigenetic characterization of single cells".

Primary LanguageRGNU General Public License v3.0GPL-3.0

The source code of RA3

DOI

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 cell clustering
  • R 3.6.1 for data visualization and downstream analyses

Usage instructions

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

License

This project is built under license GNU GENERAL PUBLIC LICENSE (GPL).