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README.md 2024-04-25 1.6 kB
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v2.1.0 source code.tar.gz 2024-04-25 18.9 MB
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v2.1.0 source code.zip 2024-04-25 19.2 MB
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  • 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    - make*_heatmap_ggplot: returned plot no longer replaces hyphens with dots    - make_mushroom_plot: additional ... parameter to pass arguments to ggplot2::theme    - make_circos_lr: added separate_legend parameter to determine whether the plot and legend are returned as separate objects    - Added nsga2R optimization functions, renamed old model evaluation functions of mlrMBO    - calculate_de: default values changed from NA to NULL    - get_exprs_avg: default values changed from NA to NULL; additional ... parameter to pass arguments to Seurat::AverageExpression    - generate_prioritization_tables: added scenario parameter
  • Revised vignettes for readability
  • parameter_optimization vignette now contains code on how to submit the job to a computing cluster
  • Added new vignette on using LIANA to construct the lignad-receptor network part of the prior model
Source: README.md, updated 2024-04-25