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add: PA clustering functions#38

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DanielGarbozo merged 4 commits intoBigMindLab:devfrom
DanielGarbozo:feature/pa_clustering
Mar 21, 2026
Merged

add: PA clustering functions#38
DanielGarbozo merged 4 commits intoBigMindLab:devfrom
DanielGarbozo:feature/pa_clustering

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New functions:

  • list_gmts
  • calc_jaccard
  • do_clust
  • get_superterm
  • get_network_communities
  • network_clust
  • network_clust_gg

Example datasets:

  • geneset_list
  • camera_results.

Vignette: pathway_analysis_clustering.
Updated: DESCRIPTION, NAMESPACE.

Rename fdr_threshold to fdr_th in calc_jaccard
Fix parameter name for FDR threshold in Jaccard calculation in all lineas
Update network_clust parameters:
Lower jaccard_threshold and min_degree for clustering
@DanielGarbozo DanielGarbozo merged commit 74015f1 into BigMindLab:dev Mar 21, 2026
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