This repo contains scripts and notebooks for spatial_analysis of MBEN data

./scripts main folder for R scripts and .ipynb, details can be found within each R script or notebook documentation

spatial_binning.R: contains code to do spatial binning given custom bin size (ie side length of a square shape)
spatial_compare_v2.ipynb: cell-level analysis
spatial_compare_mols_v2.ipynb: molecule-level (or bin-level) analysis, spatial binning of transcript coordiantes
batch correction/integration using Harmony on samples for each technology (MC, Vizgen, Xenium)
- spatial_integration_Vz_v2.R: Vizgen
- spatial_integration_Re_v1.R: MC
- spatial_integration_Xen_v1: Xenium
compute_nnn_expression.R: script that extracts expression level per section and median next nearest neighbour distance among the same transcripts
clustering and cluster analysis:
- cluster_maker.R: Performs leiden clustering on integrated samples of each technology.
- cluster_analysis.ipynb: Performs plotting of UMAPs, barplots, dotplots, heatmaps and overlays for the rulting clusters.
- neighborhood_analysis.R: Performs the permutation tests for the neighborhood analysis and plots heatmaps with p-values and z-scores.

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