Published February 7, 2022
| Version v1
Journal article
Open
Multiplexed Imaging Mass Cytometry of Chemokine Milieus in Metastatic Melanoma - Data for Analysis
Creators
- 1. University of Zurich, Department of Quantitative Biomedicine
- 2. University Hospital Zurich, Department of Dermatology
Description
The following folders/files are part of this repository:
- Zip-Archive "MelanomaIMC-Zenodo": contains all code that is available as Github release
- Folder "analysis": contains all .rmd files that are required to generate the SingleCellExperiment object with single-cell data required to reproduce all figures
- Folder "code": contains all helper functions required for the analysis pipeline
- Folder "celltype_classifier": contains scripts to load all images and masks to start the cytomapper Shiny application to generate labeled data for the random forest classifier
- Folder "helper_functions": all R helper functions (such as patch/milieu detection, etc)
- Folder "data": empty, store data folders here ("data_for_analysis" and "full_data")
- Folder "docs": all .html files generated from the scripts stored in the "analysis" folder. Contains also all panels from the figures as .pdf or .png
- Folder "output": empty
- Zip-Archive "data_for_analysis": contains processed data such as SingleCellExperiment objects, clinical data tables, labeled data for the random forest classifier, etc
- Folder "12plex_validation": data used to validate the RNAScope 12-plex system
- Folder "ClustalW_results": data used to generate Fig S6G (Sequence similarity of RNAScope targets)
- Folder "protein": all data for the Protein data set (single-cell expression data, channel order, labeled data for the random forest classifier, clinical data table, etc)
- Folder "rna": same as protein folder but for the RNA&Protein data set
- Folder "scRNAseq": scRNA-seq data required to generate Fig. S7A
- Files "sce_*.rds": R objects containing the SingleCellExperiment container with all single-cell data and metadata, used for all R analyses.
- File "HPA_rna_celline.tsv": data used to generate Fig. S3B, bulk RNA seq data from cell-lines, Human Protein Atlas
Notes
Files
data_for_analysis.zip
Files
(7.2 GB)
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md5:d59d8bda091da8bb053fa0df464595ee
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Additional details
Related works
- Is source of
- 10.5281/zenodo.6004986 (DOI)