Code for testing out various methods of cell-type deconvolution of bulk GEP data. The methods are described in the following papers:
- Abbas et al. 2009: Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns...
- Gong et al. 2011: Optimal Deconvolution of Transcriptional Profiling Data Using Quadratic Programming...
- Newman et al. 2015: Robust enumeration of cell subsets from tissue expression profiles
Download and extract the data by running ETL.ipynb. This will download the data from GEO and save it in the data directory. Anaylsis.ipynb contains the code for running the deconvolution methods and plotting the results.