Issues

• parameter n_neighbors not used in Leiden clustering for n>=11

  epigen/unsupervised_analysis#100 · Filter by author sreichl opened on Jul 23, 2026
  1

• Leiden clustering for the cosine metric fails on the test data

  epigen/unsupervised_analysis#96 · Filter by author hoferand opened on Apr 29, 2026
  1

• plot_heatmap crashing on very wide matrices (fread segfault / duplicate row-names); switching to vroom fixes it

  epigen/unsupervised_analysis#94 · Filter by author jansen-ista opened on Apr 16, 2026
  1

• implement CHOIR clustering

  enhancement
  epigen/unsupervised_analysis#77 · Filter by author sreichl opened on Mar 13, 2026

• implement Independent Component Analysis (ICA) or Non-negative Matrix Factorization (NMF)

  enhancement
  Feature

  epigen/unsupervised_analysis#75 · Filter by author sreichl opened on Oct 14, 2025
  10

  

• implement of TORQUE clustering

  enhancement
  Feature

  epigen/unsupervised_analysis#70 · Filter by author sreichl opened on Feb 15, 2025
  1

• ggrepel text for labelling of categorical Metadata in 2D plots

  enhancement
  epigen/unsupervised_analysis#68 · Filter by author sreichl opened on Nov 26, 2024

• consider adding CartoGRAPHs for visualization and DataDiVR export for VR based analysis

  enhancement
  epigen/unsupervised_analysis#42 · Filter by author sreichl opened on Jan 27, 2024

• diagnostic plot of all aggregated clustering results

  enhancement
  epigen/unsupervised_analysis#41 · Filter by author sreichl opened on Dec 20, 2023
  1

• improve data loading speed with Dask or NumPy

  enhancement
  epigen/unsupervised_analysis#37 · Filter by author sreichl opened on Dec 15, 2023

• reimplement internal cluster indices supporting different metrics and to improve performance

  enhancement
  epigen/unsupervised_analysis#33 · Filter by author sreichl opened on Oct 3, 2023

• add Variation of Information (VI) and Split/Join as external indices

  enhancement
  epigen/unsupervised_analysis#31 · Filter by author sreichl opened on Sep 27, 2023

• implement Manifold trustworthiness

  enhancement
  epigen/unsupervised_analysis#30 · Filter by author sreichl opened on Sep 22, 2023

• implement significance analysis for clustering

  enhancement
  epigen/unsupervised_analysis#29 · Filter by author sreichl opened on Sep 18, 2023
  1

• Resampling to evaluate clustering stability

  enhancement
  epigen/unsupervised_analysis#27 · Filter by author bednarsky opened on Sep 13, 2023

• clustree: investigate and implement automatic sc3 stability scoring

  enhancement
  epigen/unsupervised_analysis#24 · Filter by author sreichl opened on Sep 6, 2023

• implement consensus cluster calling

  enhancement
  epigen/unsupervised_analysis#22 · Filter by author sreichl opened on Aug 29, 2023
  1

• implement meta visualization as an aggregation of all methods (PCA, densMAP, UMAP, …)

  enhancement
  epigen/unsupervised_analysis#16 · Filter by author sreichl opened on Aug 26, 2023

• add Dynamic visualization of high-dimensional data

  enhancement
  epigen/unsupervised_analysis#15 · Filter by author sreichl opened on Aug 26, 2023

• implement partition based clustering

  enhancement
  epigen/unsupervised_analysis#14 · Filter by author sreichl opened on Aug 26, 2023

• Consider alternative clustering algorithms

  enhancement
  epigen/unsupervised_analysis#13 · Filter by author sreichl opened on Aug 25, 2023

• implement HDBSCAN clustering

  enhancement
  epigen/unsupervised_analysis#6 · Filter by author sreichl opened on Aug 25, 2023