├── .gitignore ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── analyses ├── mechanism │ ├── 02_polypharmacology.R │ ├── 03_aggregate_polypharmacology.R │ ├── 04_dge_differential_expression.R │ └── mech.R ├── predict │ ├── dge.R │ ├── genesets │ │ └── prev-ampad.gmt │ └── lit.R ├── rebuttal │ ├── .gitignore │ ├── R4-10.R │ ├── R4-4.R │ └── R4-6.R └── wrangle │ ├── DGE1.R │ ├── DGE2.R │ ├── figs.R │ ├── gset.R │ └── mayo-res.R ├── figures.tex ├── figures ├── Fig1.R ├── Fig2.R ├── Fig3.R ├── Fig4.R ├── Fig5.R ├── FigSX.R ├── Suppl1.R ├── Suppl2.R ├── Suppl3.R ├── Suppl4.R ├── Suppl5.R ├── Suppl6.R ├── Table1.R ├── Table2.R └── plot.R ├── results ├── DGE-composite.csv ├── DGE1-counts.csv.gz ├── DGE1-dfx.csv.gz ├── DGE1-meta.csv ├── DGE2-counts.csv.gz ├── DGE2-dfx.csv.gz ├── DGE2-meta.csv ├── MAYO-2019-10-10.RData ├── TAS-ecdf.csv ├── TAS-values.csv.gz ├── allpred.rds ├── cotarget_signif-2020-02-07.rds ├── deep-dye-drop.csv ├── deseq_meta.csv ├── lit-2019-10-03.RData ├── lspci_id-name-map.csv ├── normalized_counts_isg.csv ├── prev-ampad.gmt ├── results-2019-10-06.RData ├── tanimoto.csv ├── target_combo_signif-2020-02-07.rds ├── target_combos-2020-02-07.rds └── tc_signif_agg-2020-02-07.rds ├── schematics ├── Fig1A.pdf ├── Fig1B.pdf ├── Fig2A.pdf └── Fig4A.pdf ├── setup.R └── supplement.tex /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/labsyspharm/DRIADrc/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/labsyspharm/DRIADrc/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/labsyspharm/DRIADrc/HEAD/LICENSE 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