palantir 1.3.0

v1.3.0

on Python PyPI

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.