Collection of codes and annotated matrix for the paper "A cell atlas of human thymic development defines T cell repertoire formation"

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”

This repository contains:

• 'scjp' package to assist single-cell data analysis
• jupyter notebooks which show the process of analysis for all figures
• annotated, normalised matrix in h5ad format
• csv files containing the metadata
• raw count matrix in h5ad format
• vdj files (cellranger output)

The following is description for each item:

"sample_metadata_fix.xlsx" is:

• metadata for all samples generated
• contains file key for gene expression and vdj data matching (the error in previous versions are fixed here!)

"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

"HTA07.A01.v02.entire_data_raw_count.h5ad" is:

• raw count matrix for all human data generated in the study
• can be matched with annotated dataset (*.h5ad files described above) by observation names
• 'adata.obs_names' is in format of '{filename}-{cellbarcode}'

"thymus_vdj.zip" contains:

• cellranger output *.csv files for VDJ data analysis
• vdj files can be matched to gene expression files based on the information in 'sample_metadata.xlsx'
  • they should share the same cell barcode

Please also check https://github.com/Teichlab/thymusatlas for future updates

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