Palantir v1.2

[katosh]

This covers multiple changes @ManuSetty and I wrote up in preparation of our cell-state density manuscript.

Version 1.2.0

New Features

• Enable an AnnData-centric workflow for improved usability and interoperability with other single-cell analysis tools.
• Introduced new utility functions
  • palantir.utils.early_cell To automate fining an early cell based on cell type and diffusion components.
  • palantir.utils.find_terminal_states To automate finding terminal cell states based on cell type and diffusion components.
  • palantir.presults.select_branch_cells To find cells associated to each branch based on fate probability.
  • palantir.plot.plot_branch_selection To inspect the cell to branch association.
  • palantir.utils.run_local_variability To compute local gene expression variability.
  • palantir.utils.run_density A wrapper for mellon.DensityEstimator.
  • palantir.utils.run_low_density_variability. To aggregate local gene expression variability in low density.
• Added input validation for better error handling and improved user experience.

• Expanded documentation within docstrings, providing additional clarity for users and developers.

  Enhancements

• Updated tutorial notebook to reflect the new workflow, guiding users through the updated processes.

• Implemented gene trend computation using Mellon, providing more robust and efficient gene trend analysis.

  Changes

• Replaced PhenoGraph dependency with scanpy.tl.leiden for gene trend clustering.

• Deprecated the run_tsne, determine_cell_clusters, and plot_cell_clusters functions. Use corresponding implementations from Scanpy, widely used single-cell analysis library and direct dependecy of Palantir.

  Fixes

• Addressed the issue of variability when reproducing results (issue#64), enhancing the reproducibility and reliability of Palantir.