This release is for a refactored Cassiopeia codebase that includes most of the features in the original codebase and more.
Among the key improvements are:
- A more flexible preprocessing pipeline, amenable to other lineage-tracing technologies (e.g., GESTALT)
- A more streamlined & pythonic reconstruction framework, deriving from the
CassiopeiaSolver
class. This class is easily extendable for future development. - Several new algorithms implemented - for example distance-based solvers like UPGMA and graph-based solvers like MaxCut and Spectral partitioning.
- A new and improved benchmarking suite that allows for sophisticated topology and lineage-tracing simulation. In this, we have also added nuanced simulators for sampling cells, for example to simulate spatial assays.
- An improved
CassiopeiaTree
class for efficient tree manipulation and integration with transcriptomic and meta data. - Improved logging throughout.
All documentation, and tutorials are available on our documentation website here.
Any issues can be filed here.