Additional file 2 of vmrseq: probabilistic modeling of single-cell methylation heterogeneity

Additional file 2: Table S1-S9. Table S1: Performance of clustering cells in Luo et al. [12] data with VMRs overlapped with targeted features. Default parameters, g = 100 and $$\theta = 0.7$$ θ = 0.7 , were used for calculation of the nearest neighbor score. The ‘broad classes’ refer to the 2 broad neuronal classesin Luo et al. [12] data, and ‘subtypes’ refer to 15 subtypes within those two classes. Gene promoters were defined as $$pm 2$$ p m 2 -kb windows around the transcription start sites of genes extracted from ENSEMBL version 80 [55]. Additional File 2: Table S9 lists data sources of the histone ChIP-seq annotation information. Table S2: Table with sample metadata from the mouse frontal cortex dataset. Table S3: Table with sample metadata from the multi-omic mouse gastrulation dataset. Table S4: Table with the correlation between gene expression and VMR/promoter methylation. Table S5: Table with the subtypes included in training parameters in transition probability and emission probability used as default in this study. Table S6: Table with the trained transition probability. Table S7: Table with the trained beta prior parameters of the emission probability for methylated grouping. Table S8: Table with the trained beta prior parameters of the emission probability for methylated grouping. Table S9: Table with data sources of histone ChIP-seq annotation information used in the experiments.