https://github.com/mskcc/chl-spatial-profiling

Code supporting results of cHL manuscript
https://github.com/mskcc/chl-spatial-profiling

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Code supporting results of cHL manuscript

• Host: GitHub
• URL: https://github.com/mskcc/chl-spatial-profiling
• Owner: mskcc
• Created: 2024-02-13T22:41:32.000Z (10 months ago)
• Default Branch: main
• Last Pushed: 2024-05-30T17:56:13.000Z (7 months ago)
• Last Synced: 2024-05-30T20:57:56.656Z (7 months ago)
• Language: R
• Homepage:
• Size: 4.39 MB
• Stars: 1
• Watchers: 6
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Spatial profiling of classic Hodgkin lymphoma (cHL)

#### Code supporting manuscript:

#### *Multiplexed spatial profiling of Hodgkin Reed-Sternberg cell neighborhoods in classic Hodgkin lymphoma*

## Multiplexed IF analysis

- Install `snakemake`, `R 4.0.2`, and all libraries in `statistics/source_all.R`.

- For reformatting of HALO output (csv files) to `RDA` files, please reference: https://github.com/mskcc/cHL-pre-processing. This is a fork of `HaloX` repo branch `ver/halo_v3.5.1`.

- `scripts/misc` contains R scripts for cell reassignments, UMAP clustering, and HRS aggregate analysis. `reassignment_rules.md` contains cell reassignment hierarchy. 

- `statistics` contains R scripts for all statistical analyses.

## Bulk transcriptomic analysis

- `NanoString/hodgkin_rna_analysis.Rmd` contains all code for analysis of RNA sequencing data and generation of paper figures. 

## Raw data

- Please reference: https://zenodo.org/records/10659311

- Contains raw multiplexed IF data and files referenced in `NanoString/hodgkin_rna_analysis.Rmd`.