NOTE: in order to apply the DECCODE approach to your custom profiles, you need to have: 1) drug-induced pathway-based expression profiles (PEPs), 2) cell type PEPs. You can download pre-computed drug-induced PEPs from here. Gene expression profiles must be differential. In order to convert your gene expression profiles to PEPs you can use the gep2pep R/Bioconductor package. Once you have 1 and 2, you can simply match drug induced to cell type PEPs using a proper distance, such as Manhattan. Publication: https://doi.org/10.1016/j.stemcr.2021.03.028 This release includes: plate scans.zip: 5 images (15 plates) from secondary reprogramming experiments (single drugs). 1 Excel file identifying treatments and controls in the plates above. 1 image (5 plates) from primary reprogramming experiments with Tazobactam (directly annotated). plate scans - drug pairs.zip 3 plate scan images from experiments with drug pairs. 1 PDF file identifying treatments in the plates above. 1 TXT file containing the used ImageJ parameters for counting. ColonyCountingScripts.zip Matlab scripts used to automatically extract well images from plate scans (secondary reprogramming) ImageJ macro used to count colonies in the extracted well images rankedLINCSprofiles_ testedDrugs_cellClusters.xls full list of LINCS expression profiles including DECCODE scores and pluripotency. list of all tested drugs cell type clusters top-30_pairs_20_each.xlsx Top 30 drugs that once paired with other drugs achieve highest scores as computed by the drug-combinations approach. The top 20 pairs are reported for each of the 30 starting drugs.