Introduction | Reproducibility | Data description | Data preprocessing | Data import | Data transformation | Data organization | Diagnostic plots | MDS plot | Marker ranking based on the non-redundancy score | Cell population identification with FlowSOM and ConsensusClusterPlus | Visual representation with UMAP | Cluster merging and annotation | Manual cluster merging and annotation based on heatmaps | Reducing the number of clusters in ConsensusClusterPlus | Comparison of automated and manual merging | Differential analysis | Differential cell population abundance | Differential analysis of marker expression stratified by cell population | Differential analysis of overall marker expression | Obtaining higher resolution | Discussion | Software availability | Author contributions | Competing interests | Grant information | Acknowledgments | References

Introduction | What is allele-specific methylation? | Overview | Why SNP-based? | Why tuple-based? | Installation | Get bam files | SNP-based (aka slow-mode) | Example Workflow | Obtain allele-based methylation calls | Summarize methylation calls across samples | Find DAMEs | tuple-based (aka fast-mode) | Run Methtuple on bam files | Read methtuple files | Calculate ASM Score | Visualization | DAME tracks | Methyl-circle plot | MDS plot | Session Info | References