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pathfindR 2.4.0
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@egeulgen egeulgen released this 28 Apr 22:41
v2.4.0
caf8e3d
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egeulgen Ege Ulgen
GPG key ID: A3D82C7AD8E1A572
Learn about vigilant mode.

Major Changes

  • implemented a new color_kegg_pathway() function using ggkegg to create colored KEGG pathway ggplot objects (instead of using KEGGREST to obtain the colored PNG files, which no longer works #169)
  • renamed the visualize_hsa_KEGG function to visualize_KEGG_diagram() to reflect this is now able to handle KEGG pathway enrichment results from any organism
  • updated the visualize_terms(), visualize_term_interactions() and visualize_KEGG_diagram() functions so that they now return a list of ggplot objects (named by term ID)
  • updated the get_kegg_gsets() function to also use ggkegg for fetching genes per pathway data
  • removed unneeded dependencies: magick, KEGGgraph and KEGGREST

Minor Changes and Bug Fixes

  • updated the get_biogrid_pin() function so that it can now determine the latest version and download/process it from BioGRID (via setting release = "latest", which is now the default behavior)
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