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README.md

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- `compute_nnn_expression.R`: script that extracts expression level per section and median next nearest neighbour distance among the same transcripts
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- clustering and cluster analysis:
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- `cluster_maker.R`: Performs leiden clustering on integrated samples of each technology.
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- `cluster_analysis.ipynb`: Performs plotting of UMAPs, barplots, dotplots, heatmaps and overlays for the rulting clusters.
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- `cluster_analysis.ipynb`: Performs plotting of UMAPs, barplots, dotplots, heatmaps and overlays for the rulting clusters.
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- `neighborhood_analysis.R`: Performs the permutation tests for the neighborhood analysis and plots heatmaps with p-values and z-scores.

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