Minor Changes and Bug Fixes

• Moved org.Hs.eg.db from "Imports" to "Suggests" per new CRAN policy. Relevant functions revert to default behaviour if the required package is not installed.

Minor Changes and Bug Fixes

• fixed missing argument issue in get_gene_sets_list(#230)
• refactored to introduce safe_get_content so that URL access issues are handled more gracefully

Minor Changes and Bug Fixes

• fixed NA values in kappa matrix generation that will cause error as part of the latest igraph update (#227)

Major Changes

• updated dependencies so that pathfindR depends on msigdbr (>= 24.1.0)
• added the new db_species argument to the get_mgsigdb_gsets() data generation function

Minor Changes and Bug Fixes

• fixed test assertions that will break as part of the latest ggplot2 update (#223)

Minor Changes and Bug Fixes

• fixed a bug in visualize_KEGG_diagram() where ggkegg was raising an error (#214)

Minor Changes and Bug Fixes

• fixed a bug regarding KEGG gene set fetching: removed the conversion functionality in get_kegg_gsets() which now returns KEGG IDs so that the user can convert the returned identifiers using a more appropriate tool (e.g. BioMart) should they wish

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)

Minor Changes and Bug Fixes

• fixed a bug in the UpSet_plot() plot function regarding the interaction with ggupset package that was discovered in a reverse dependency check for ggplot2 3.5.0 (#189)
• fixed gene symbol case mismatch issue in score_terms() (#186)
• applied enhancement suggestion from #184 to enable scale fill manual for term_gene_graph()

Major Changes

• reverted removal of create_HTML_report() so run_pathfindR() once again generates HTML reports

Minor Changes and Bug Fixes

• added the disable_parallel argument in active_snw_enrichment_wrapper() to be able to disable parallel runs via foreach
• fixed the issue encountered on CentOS where forech wasn't loading pathfindR (#164)
• fixed a CRAN error due to a package documentation issue (#172)
• performed some refactoring and updated/improved all tests