redeem_reproducibility

Analysis reproducibility of paper (Weng et al., 2024, Nature) "Deciphering cell states and genealogies of human hematopoiesis"

Notes

• Note-1 ReDeeM development and optimization.ipynb
• Note-2 Single-cell deep mtDNA mutation detection quality control.ipynb
• Note-3 Benchmark ReDeeM using Crispr-based lineage tracing.ipynb
• Note-4 Human Hematopoiesis ReDeeM.ipynb
• Note-5 HSC clonal structure and heterogeneity.ipynb
• Note-6 HSC clonal output analysis.ipynb

Data availability

Raw data are availble GSE219015

Software availability

• redeemV is set of in-house Bash pipeline and Python scripts for mapping and deep mitochondrial mutation calling.
• redeemR is an in-house R package for downstream lineage tracing and single cell integrative analysis.

Update

2024-1-22: We are still working on Note-7 Clonal architecture alteration in aging and some intermediate data sharing. We will update as soon as these are ready. Thank you!

Citation

Please check out the paper Deciphering cell states and genealogies of human hematopoiesis

Contact

If you have any questions or suggestions, please feel free to contact us. Feedbacks are very welcome! (Chen Weng, cweng@broadinstitute.org)