This is the collection of codes and annotated matrix described in the paper “A cell atlas of human thymic development defines T cell repertoire formation” NEW VERSION AVAILABLE - PLEASE CHECK 10.5281/zenodo.3711134 This repository contains: 'scjp' package to assist single-cell data analysis jupyter notebooks which show the process of analysis for all figures annotated matrix in h5ad format csv files containing the metadata sample_metadata.xlsx: metadata for all samples generated "thymus_code_package.zip" contains: *.ipynb: jupyter notebooks describing the analysis F00_global_variables.py: contains global variables shared across multiple notebooks scjp: python package to support the single-cell analysis (not for the distribution, there are some dependency issue that needs to be fixed. Final version is under-preparation.) "thymus_annotated_matrix_files.zip" contains: *.csv: metadata including annotation per cell (.obs in scanpy anndata) *.h5ad: anndata containing matrix for normalised read counts, metadata including annotation per cell (use python scanpy package for navigation. See 'Data_navigator.ipynb' for tutorial) Data_navigator.ipynb: jupyter notebook describing each dataset Please also check https://github.com/Teichlab/thymusatlas This github repository will be used to update any additional materials which are not covered in here. Please contact to: jp24@sanger.ac.uk or jepark87@gmail.com for any questions