README.md

Data pre-processing

The pre-processed data files can be reproduced from the files provided in the original datasets using the corresponding jupyter notebooks provided here. If you want to skip this step, you can also download them here and add them to the preprocessed directory.

A few special case:

• The lineage trees published with the mouse embryogenis dataset from from Chan et al. are missing cell lables. We used additional files that we received to from the authors to resolve the labels for embryo 2 and the lineage tree from the HotSpot tutorial for embryo 3 and provided the labeled trees directly in the mouse directory.
• Not all cells in the C. elegans dataset from Packer et al. had cell type annotations. We filled in the missing types based on this list from Sulston et al. and provide a table of them in the worm directory.