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v1.3.0
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@ManuSetty ManuSetty released this 03 Jul 19:03
· 81 commits to master since this release
v1.3.0
1cccc3a

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_density_evaluation Evaluate computed density on a different dataset.
    • palantir.utils.run_low_density_variability. To aggregate local gene expression variability in low density.
    • palantir.plot.plot_branch. To plot branch-selected cells over pseudotime in arbitrary y-postion and coloring.
    • palantir.plot.plot_trend. To plot the gene trend ontop of palantir.plot.plot_branch.
  • 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.
  • Enable annotation in palantir.plot.highight_cells_on_umap.

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.
  • Rename palantir.plot.highight_cells_on_tsne to palantir.plot.highight_cells_on_umap
  • Depend on anndata>=0.8.0 to avoid issues writing dataframes in ad.obsm.

Fixes

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