Welcome!#

This website serves as documentation to the Cassiopeia software suite, maintained by the Yosef Lab at the Weizmann Institute.

Cassiopeia [Jones20] is a package for end-to-end phylogenetic reconstruction of single-cell lineage tracing data. The package is composed of the following modules:

  • preprocess for processing sequencing FASTQ data to character matrices.

  • solver for performing tree inference.

  • simulator for simulating trees and character-level data.

  • plotting for plotting trees.

  • spatial for performing analyses with spatial data.

  • tools for analyzing phylogenies, for example with paired RNA-seq data.

If you find this useful for your research, please consider citing Cassiopeia [Jones20].

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Installation

New to Cassiopeia? Check out the installation guide.

To the installation guide

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User guide

The tutorials provide in-depth information on running Cassiopeia.

To the user guide

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API reference

The API reference contains a detailed description of the Cassiopeia API.

To the API reference

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Questions & Issues

Have a question or found a bug? File an issue.

File an issue

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