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Code for the paper "Clonal analysis reveals spatial determinants of progenitor fates in embryos"

A repository with code and analysis for the paper Erickson, Isaev et al.

Folders description

  • 00_QC contains notebooks for the quality control of each sample with corresponding pdf-reports (subfolder QC_reports),
  • 01_Embedding_construction contains notebooks in which we're building gene expression embeddings and annotate them before adding the layer with clonal information,
  • 02_Fate_distribution contains clonal analysis and further hypothesis testing,
  • 03_Perturbations contains a functional and compositional analysis of the results of mosaic perturbations at single-cell and whole clone levels,
  • Supplementary contains some of the additional analysis for the paper,
  • tools contains additional functions that are used in Jupyter notebooks.

Additional data sources

  • Raw reads and Cell Ranger outputs are reachable via GEO,
  • Modified TREX algorithm (original) for clonal barcodes calling is stored on GitHub,
  • AnnData objects (both clonal and gene expression) and plasmid maps (for chimeric references construction) are available on Zenodo,
  • Python package scLiTr that was used for the analysis is available on GitHub,
  • Interactive Cellxgene web-explorer is located on on Adameyko lab private Cellxgene browser,
  • Interactive web-app clones2cells for simultanious clonal and gene embedding exploration is available on Streamlit Cloud.

Please don't hesitate to contact me via sergey.isaev[at]meduniwien.ac.at if you have any questions regarding the code or gene expression / clonal objects from the paper.