pycea.datasets.packer19

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pycea.datasets.packer19#

pycea.datasets.packer19(cache_dir='~/.treedata/datasets', tree='full')#

C elegans lineage tree with cell state and position [PZH+19].

In this study, single-cell RNA sequencing (scRNA-seq) was performed on C. elegans embryos at various developmental stages. Using computational methods, gene expression patterns from the literature, and fluorescent reporter lines, single cells were then mapped to their position in the known C. elegans lineage tree. This dataset contains the average expression of each cell across the lineage tree with corresponding spatial coordinates from [RZW+13].

Parameters:

  • cache_dir (PathLike | str (default: '~/.treedata/datasets')) – The directory where the datasets are cached. Default is ~/.treedata/datasets.

  • tree (Literal['full', 'observed'] (default: 'full')) – The tree to load. If “full”, the full lineage tree is used. If “observed”, the tree is pruned to only include lineages that are resolved by Packer et al. 2019 at the 400 minute time point.

Return type:

TreeData

Returns:

TreeData object.

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