anndata with trees
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TreeData - AnnData with trees
TreeData is a lightweight wrapper around AnnData which adds two additional attributes, obst and vart, to store nx.DiGraph trees for observations and variables. TreeData has the same interface as AnnData and is fully compatible with scverse packages like Scanpy.
To learn more about TreeData, please refer to the documentation or checkout the getting started guide.
See the Pycea documentation to learn how TreeData can be used to analyze single-cell lineage tracing data.
Installation
You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.
There are several alternative options to install treedata:
- Install the latest release of
treedatafrom PyPI:
pip install treedata
- Install the latest development version:
pip install git+https://github.com/YosefLab/treedata.git@main
Release notes
See the changelog.
Contact
For questions and bug reports please use the issue tracker.
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t.b.a
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