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Maizels2023aa

Code for analysis for:

Deep dynamical modelling of developmental trajectories with temporal transcriptomics Rory J. Maizels, Daniel M. Snell, James Briscoe

Input data not available here due to size: adata files created in notebooks A0.0 and A0.1 are available in GEO (GSE236520) and will soon be available to download directly with the velvet package (https://github.com/rorymaizels/velvet). Alternatively, raw fastqs can be downloaded and processed using dynast (https://github.com/rorymaizels/sciFATE2_processing) to give the input data to notebooks A0.0 and A0.1.

The full, processed, cell-typed data used for analysis can be downloaded here: https://www.dropbox.com/s/wyca8asv8r32sui/celltyped_adata.h5ad?dl=0