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cHSPCTrack - clonal Hematopoietic Stem and Progenitor cells tracker

This repository contains the code used to produce the results shown in our joint Shlush & Tanay lab manuscript "Human HSPCs clones balance stochastic diversification with cytokine-induced differentiation" (Elia Colin,*, Dror Brook,*, Jonathan Izraeli, Oren Milman, Aviezer Lifshitz, Tal Bachrach, Noa Chapal-Ilani, Liran Shlush,**, Amos Tanay,**).

Data availability

All data required to reproduce the figures are available at:

s3://chspctrack/cHSPCTrack/

After cloning the code repository, the data should be downloaded into the data/ directory at the root of the repository using:

mkdir -p data
aws s3 sync s3://chspctrack/cHSPCTrack ./data --no-sign-request

Expected structure:

data/
  clonal_memory_data/
  differentiation_rate_data/
  other_datasets/
  tags_data/
  cell_type_colors.csv
  cells_with_clone_info.h5ad
  gene_modules_dict.pkl
  metacells.h5ad
  trajectory_pc_mapper.pkl