This repo contains multiple tools to perform retrospective lineage tracing and call cell type information from the same single cell using microsatellite and methylation, respectively. Below is a summary of the analysis tools developed.
Paper published in Genome Research, doi:10.1101/gr.255851.119
- HipSTR_allelotype: Run HipSTR for microsatellite calling and allelotyping
- Custom_allelotype: Run scripts for custom microsatellite calling and allelotyping (based off of LobSTR)
- merge_allelotype: Merge multiple alleleDict pickle files from either Custom or HipSTR allelotyping
- buildPhylo: Build phylogenetic tree given allelotype of single cells
- iterPhylo: Iteratively build phylogenetic tree given allelotype of single cells
- evalPhylo: Evaluate accuracy of phylogeny given exVivo tree data
- viewPhylo: Utilize ete3 to view phylogenetic tree derived from buildPhylo
- importMethyl: Import methylation calls derived from methylpy TSV files for samples/cell type ref (make sure to run methylpy prior to import)
- refPD: Calculate and plot pairwise dissimilarity between single cells and reference cell types
- pairwise_methRate: Calculate methRate across Ensembl Regulatory Build windows
- combinedPhylo: Build phylogenty by combining MS and Methyl distances between single cell pairs