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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.