Data for reproducing Webster figures

# Data for reproducing Webster figuresThis zip file contains the file structure and input data for plugging into the Webster figure generation code repo (https://github.com/joshbiology/gene_fn).For flat files and Excel spreadsheets containing the actual output of Webster, see our other Figshare (10.6084/m9.figshare.14963561).This folder is strucured as follows:```data├── interim│ ├── biomarker│ └── matlab│ ├── depmap_deep│ ├── depmap_denoise│ ├── depmap_grid│ ├── depmap_wide│ ├── durocher│ ├── durocher_no_graph│ └── synthetic└── raw ├── depmap ├── durocher ├── genesets ├── hart ├── humancellmap ├── nusiance_genesets └── prism```## rawThis folder contains tables from other resources, described below.* depmaphttps://depmap.org/* durocherhttps://pubmed.ncbi.nlm.nih.gov/32649862/* genesetsCustom genesets from:* * STAGA/ATAC complexes (Spedale et al., 2012)* * SWI/SNF complexes (Mashtalir et al., 2018).* * Mediator complex (Tsai et al., 2014). * * Integrator complex (Pfleiderer and Galej, 2021; Sabath et al., 2020; Tilley et al., 2021; Zheng et al., 2020)* hartCommon essential genesets from Hart et al. 2015* humancellmapSubcellular localization info from https://humancellmap.org/ and Go et al. 2021.* nusiance_genesetsGenesets from HUGO.* prismCompound sensitivity data from https://depmap.org/repurposing/ and Corsello et al 2020.## interimThis folder contains MATLAB files (.mat) that are the output of the dual-graph regularized dictionary learning applied with this codebase (https://github.com/joshbiology/graph_dictionary_learning) on preprocessed input data contained here (10.6084/m9.figshare.14963561).* depmap_deepInput: DepMap data. Output: sweep over a few values of k, at t=4 and multiple random seeds.* depmap_denoiseInput: DepMap data with added noise. Output: Dictionaries (k=220, t=4) learned on noisy DepMap data.* depmap_gridInput: DepMap data. Output: sweep over many values of k and t.* depmap_wideInput: DepMap data. Output: sweep over many values of k, and t = 4 and the same random seed.* durocherInput: genotoxic fitness data (Olivieri et al 2020). Output: sweep over many values of k, at t=1,2.* durocher_no_graphInput: genotoxic fitness data (Olivieri et al 2020). Output: sweep over many values of k, at t=1,2, with alpha and beta set to 0. * syntheticInput: Synthetic fitness data.VersionsV1: Initial commitV2: Cached additional intermediate data in the interim folder.