This repository has (slightly cleaner) versions of the code we used to compare single cell sequencing data with different sequencing platforms. More documentation will be added.

ComparePackage_R is the R code we used for downstream analysis, turned into a R package (version for the paper was just individual scripts)

ExtendedRef contains the nextflow pipelines we used for creating an extended reference with either single cell or bulk data (hope to combine into a single pipeline at some point)

Preprocessing contains scripts used for different preprocessing steps, such as Vireo, downsampling, etc.

PythonScripts contains numerous python scripts used for analysing different parts of the data.