Typewriter analysis

NOTE This is a preliminary repository. We now keep all code related to SciPhy in the repo: https://github.com/seidels/sciphy-materials

Typewriter is a an experimental technique to acquire lineage tracing data. Find the publication here. This repository contains code written for basic analysis of the edited barcode sequences as well as code to simulate, process and analyze this data using phylogenetic inference software BEAST2.

1. exploratory analysis: exploring basic features of the editing process: rates/probabilities for trinucleotides/TargetBCs
2. simulation: Code for simulating the tree; Code/Ideas on how to get priors on parameters based on the HEK data and paper
3. validations: well-calibrated simulations on a fixed tree for improving versions of the model implementation
4. cell culture analysis: Code analysing the HEK cell culture data
5. preliminary gastruloid analysis