Published November 4, 2020 | Version v1
Journal article Open

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

Authors/Creators

  • 1. UCSF / Inscripta
  • 2. UCSF / UC Berkeley
  • 3. UCSF
  • 4. UCSF / Princeton
  • 5. UC Berkeley
  • 6. UCSF / MIT

Description

Central code modules for analyzing the lineage tracing data in our manuscript entitled "Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts".  The code stored in this repository contains notebooks for repeating main analyses, as well as scripts and utilities. The majority of the code is written for >= Python 3.5, though there are some other files written in Julia and R. Other specific methodology can be found in the supplementary methods of our manuscript.

Other software used in this study are publicly available, including:

Cassiopeia (https://github.com/YosefLab/Cassiopeia)

Hotspot (https://github.com/YosefLab/Hotspot)

scVI (https://github.com/YosefLab/scvi-tools)

 

Files

MetastasisTracing-master.zip

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