Collection of codes and annotated matrix for the paper "A cell atlas of human thymic development defines T cell repertoire formation"
- 1. Sanger Institute
- 2. Newcastle University
- 3. Ghent University
Description
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.xlsx" is:
- metadata for all samples generated
- contains file key for gene expression and vdj data matching
"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
Files
thymus_annotated_matrix_files.zip
Files
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