https://github.com/mskcc/chl-spatial-profiling
Code supporting results of cHL manuscript
https://github.com/mskcc/chl-spatial-profiling
Last synced: 5 months ago
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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 (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-05-30T17:56:13.000Z (about 2 years ago)
- Last Synced: 2025-07-18T07:43:33.648Z (11 months ago)
- Language: R
- Homepage:
- Size: 4.39 MB
- Stars: 1
- Watchers: 6
- Forks: 1
- Open Issues: 0
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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`.