pathfindR 1.5.0 2020-06-06

Major Changes

  • created separate package pathfindR.data for storing pathfindR data
  • added the function visualize_active_subnetworks() for visualizing graphs of active subnetworks
  • add the new vignette “Comparing Two pathfindR Results” that briefly describes how different pathfindR results can be compared
  • added the functions combine_pathfindR_results() and combined_results_graph() for comparison of 2 pathfindR results and term-gene graph of the combined results, respectively
  • added the function get_pin_file() for obtaining organism-specific PIN data (only from BioGRID for now)
  • added the function get_gene_sets_list() for obtaining organism-specific gene sets list from KEGG, Reactome and MSigDB
  • added the function term_gene_heatmap() to create heatmap visualizations of enriched terms and the involved input genes. Rows are enriched terms and columns are involved input genes. If genes_df is provided, colors of the tiles indicate the change values
  • added the function UpSet_plot() to create UpSet plots of enriched terms
  • added the human cell markers gene sets data cell_markers_gsets and cell_markers_descriptions

Minor changes and bug fixes


pathfindR 1.5.1 2020-09-20

Minor changes and bug fixes