Issues

• find a way to get the metadata that ports over to xenium explorer, alphabetized!

  RaredonLab/NICHESv2#29 · Filter by author diegospa99 opened on Nov 12, 2025

• migrate the plot insets function diego made in his pplr config file to NICHESv2

  RaredonLab/NICHESv2#28 · Filter by author diegospa99 opened on Nov 11, 2025

• consider ways to package edge and node data?

  RaredonLab/NICHESv2#27 · Filter by author diegospa99 opened on Nov 11, 2025
  1

• consider whether NICHESv2 should depend on seurat at all...

  RaredonLab/NICHESv2#26 · Filter by author diegospa99 opened on Nov 11, 2025
  1

• consider how best to store index and handle niches data

  RaredonLab/NICHESv2#25 · Filter by author diegospa99 opened on Nov 11, 2025

• integrate the mindmaps as part of the edge coloring

  RaredonLab/NICHESv2#24 · Filter by author diegospa99 opened on Nov 11, 2025

• make some functions to make C2C data heatmaps

  RaredonLab/NICHESv2#23 · Filter by author diegospa99 opened on Nov 11, 2025

• build some fundamental plotting functions tuned for NICHES data

  RaredonLab/NICHESv2#22 · Filter by author diegospa99 opened on Nov 11, 2025

• make C2S / S2C non dependent on C2C

  RaredonLab/NICHESv2#21 · Filter by author diegospa99 opened on Nov 11, 2025

• make nonspatial C2C more flexible / user customizable

  RaredonLab/NICHESv2#20 · Filter by author diegospa99 opened on Nov 11, 2025

• make N2C2N part of niches, with good underlying logic

  RaredonLab/NICHESv2#19 · Filter by author diegospa99 opened on Nov 11, 2025

• make C2C as a dedicated step that always runs

  RaredonLab/NICHESv2#18 · Filter by author diegospa99 opened on Nov 11, 2025

• allow easy and rapid mapping of (new) cell metadata to previously-omputed NICHES assays

  RaredonLab/NICHESv2#17 · Filter by author diegospa99 opened on Nov 11, 2025

• make the tissue graph construction independent from the rest of the workflow

  RaredonLab/NICHESv2#16 · Filter by author diegospa99 opened on Nov 11, 2025

• add a tagging feature on the landmark zones function.

  RaredonLab/NICHESv2#15 · Filter by author diegospa99 opened on Nov 11, 2025

• initialize LocalNeighborhoodPlot function

  RaredonLab/NICHESv2#11 · Filter by author msraredon opened on Nov 5, 2025

• Build CTC spatial plotting function

  RaredonLab/NICHESv2#10 · Filter by author diegospa99 opened on Nov 4, 2025

• properly format the createNeighborhoodAssay

  RaredonLab/NICHESv2#8 · Filter by author diegospa99 opened on Nov 4, 2025