Simulated multi-omics datasets based on ovarian cancer (generated with InterSIM R library)

This dataset contains synthetic multi-omics data generated using the InterSIM R package. The simulations produce three omics layers, gene expression, DNA methylation, and protein expression, with cluster overlap controlled by an "effect size" parameter. Each simulation is parameterised by a random seed (controlling reproducibility) and an effect size (controlling the degree of separation between clusters). Twenty effect sizes are tested per seed, ranging from 0.1 (minimal cluster separation) to 2.0 (maximal cluster separation) in increments of 0.1. A total of 30 seeds are used (43–62 and 73–82), yielding 600 simulation combinations in total. File contents expr.csv — Simulated gene expression data matrix (samples × genes). methyl.csv — Simulated DNA methylation data matrix (samples × CpG sites). protein.csv — Simulated protein abundance data matrix (samples × proteins). labels.csv — Cluster membership labels assigned to each sample by the simulation. pca_expr.png — PCA plot of the gene expression layer. pca_methyl.png — PCA plot of the DNA methylation layer. pca_protein.png — PCA plot of the protein abundance layer. Each PCA plot visualises the cluster structure induced by the specified effect size for the corresponding omics layer. Folder structure root/ ├── seed43/ │ ├── effect_0.1/ │ │ ├── expr.csv │ │ ├── labels.csv │ │ ├── methyl.csv │ │ ├── protein.csv │ │ ├── pca_expr.png │ │ ├── pca_methyl.png │ │ └── pca_protein.png │ ├── effect_0.2/ │ │ ├── expr.csv │ │ ├── labels.csv │ │ ├── methyl.csv │ │ ├── protein.csv │ │ ├── pca_expr.png │ │ ├── pca_methyl.png │ │ └── pca_protein.png │ ├── ... │ └── effect_2.0/ │ ├── expr.csv │ ├── labels.csv │ ├── methyl.csv │ ├── protein.csv │ ├── pca_expr.png │ ├── pca_methyl.png │ └── pca_protein.png ├── seed44/ │ └── ... ├── ... ├── seed62/ │ └── ... ├── seed73/ │ └── ... └── seed82/ └── ... Generation All data were simulated using the InterSIM package in R. Chalise P, Raghavan R, Fridley BL. InterSIM: Simulation tool for multiple integrative 'omic datasets'. Comput Methods Programs Biomed. 2016 May;128:69-74. doi: 10.1016/j.cmpb.2016.02.011. Epub 2016 Feb 27. PMID: 27040832; PMCID: PMC4833453. License CC0 1.0 Universal (public domain dedication)