Genetic Characterization of the Cell Types of in Developing Feathers, and the Evolution of Feather Complexity

This repository contains the code necesary to reproduce the analysis done for Limber et al. Genetic Characterization of the Cell Types of in Developing Feathers, and the Evolution of Feather Complexity. scRNAseq data files can be found at GEO: GSE275984Merged_Analysis contains code to process plucked feather datasets. Feather_Skin contain code to process the feather and skin sample. Evoultionary_Tree contains the code to create and plot the tree found in the paper and relies on processed data from Merged_Analysis and uses the annotations_deduplicated.xlsx. Plots contains code to reproduce plots found in the paper and relies on Merged_Analysis and Feather_Skin. RNA_Velocity.ipynb requires running the Merged_Analysis and will also require the loom files included in this repository.