saeyslab/nichenetr

📋 Changes

• Fixed `make_line_plot()` bugs (#273)
• Fixed `get_exprs_avg()` when cell types have underscores in their names (#274)
• Bug fixes for `assign_ligands_to_celltype()` (#275, #277)
• Fixed mistakes in `generate_info_tables()` (grouping metadata and filtered lr network) (#279)
• Replaced the GitHub Actions workflow file with something simpler (`.github/workflows/check-standard.yaml`) (#290)
• Removed limma from the list of dependencies (#290)
• Updated `alias_to_symbol_seurat()` (#299)
• Changed defaults of `generate_prioritization_tables()`: activity_scaled weight is set to 1 by default, and the cell type specificity weights are downweighted (#300)
• + 1 more

📋 Changes

• tidyverse is now a dependency
• New helper functions:
• General: `get_weighted_ligand_receptor_links`, `prepare_ligand_receptor_visualization`, `make_line_plot`
• Circos plot/chord diagram: `assign_ligands_to_celltype`, `get_ligand_target_links_oi`, `prepare_circos_visualization`, `make_circos_plot`
• Prioritization: `generate_info_tables`
• Changes to existing functions:
• `get_lfc_celltype`: removed `expression_pct` parameter, replaced with `...` where arguments can directly be provided to `Seurat::FindMarkers`
• `get_ligand_signaling_path`: added `minmax_scaling` parameter to scale the weights of signaling and regulatory networks
• + 10 more

📋 Changes

• Fixed `get_expressed_genes` compability issue with Seurat v5

📋 Changes

• Compatibility issue with Seurat v5
• Subsetting bug with `calculate_de`