Published August 2, 2023
| Version 1.0.0
Journal article
Open
Spatial subsetting enables integrative modeling of oral squamous cell carcinoma multiplex imaging data
Creators
- Einhaus, Jakob1
- Gaudilliere, Dyani1
- Hedou, Julien1
- Feyaerts, Dorien1
- Ozawa, Michael G.1
- Sato, Masaki1
- Ganio, Edward A.1
- Tsai, Amy S.1
- Stelzer, Ina A.1
- Bruckman, Karl C.1
- Amar, Jonas N.1
- Sabayev, Maximilian1
- Bonham, Thomas A.1
- Gillard, Joshua1
- Diop, Maïgane1
- Cambriel, Amelie1
- Mihalic, Zala N.1
- Valdez, Tulio1
- Liu, Stanley Y.1
- Feirrera, Leticia2
- Lam, David K.2
- Sunwoo, John B.1
- Schürch, Christian M.3
- Gaudilliere, Brice1
- Xiaoyuan, Han2
- 1. Stanford University School of Medicine
- 2. University of the Pacific, Arthur A. Dugoni School of Dentistry
- 3. University of Tübingen School of Medicine
Description
The following folders/files are part of this repository:
Zip-Archive "OSCC-IMC-Einhaus2023" contains all the data and code necessary reproduce all analysis steps:
- Folder "UOPCohort": Contains all data and code regarding the OSCC cohort collected at UOP.
- Folder "Dataframes": All output dataframes produced in the script "Analysis_UOP.Rmd".
- Folder "Metadata": Existing clinical metadata and output files of the folder "Tumormasks".
- Folder "Steinbock": Raw data and single-cell segmentation output after Steinbock segmentation.
- Folder "Tumormasks": All scripts necessary to generate tumormasks, measure celldistances from the tumorborder, and calculate zonal areas. Output files are stored in the folder "Metadata".
- Script "Analysis_UOP.Rmd": Code for cell phenotyping and feature matrix generation.
- Folder "STACohort": Contains all data and code regarding the OSCC cohort collected at STA.
- Folder "Dataframes": All output dataframes produced in the script "Analysis_STA.Rmd".
- Folder "Metadata": Existing clinical metadata and output files of the folder "Tumormasks".
- Folder "Steinbock": Raw data and single-cell segmentation output after Steinbock segmentation.
- Folder "Tumormasks": All scripts necessary to generate tumormasks, measure celldistances from the tumorborder, and calculate zonal areas. Output files are stored in the folder "Metadata".
- Script "Analysis_STA.Rmd": Code for cell phenotyping and feature matrix generation.
- Folder "AnalysisMultivariate": Code required to reproduce the multivariate model generated.
- Input data is pulled from the folder "UOPCohort".
- Folder "Model": Output data produced by the Jupiter notebook "Model.pynb".
- Folder "stabl": Contains a modified Python package (STABL).
- Folder "AnalysisUnivariate": Code required to reproduce the univariate analysis of all features. Input files are pulled from the folders "STACohort" and "UOPCohort".
- Folder "Visualization": Code required to reproduce figure 1-6 and supplemental figures 1-11. Input files for visualization are pulled from the folders "STACohort" and "UOPCohort".
PDF "OSCC-IMC-SupplementalMaterial" contains supplemental tables and figures.
Files
OSCC-IMC-Einhaus2023.zip
Files
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