HTTPS SSH
# eADAGE This repository is in support of the eADAGE paper. It contains all the code and necessary data/metadata to repeat all analyses in the paper. ## What is eADAGE? eADAGE (ensemble ADAGE) is an enhanced version of [ADAGE](https://github.com/greenelab/adage). It consolidates 100 individual ADAGE models into one ensemble model. eADAGE automatically extracts biologically meaningful features from large-scale transcriptomic data. ## How do I repeat analyses in the eADAGE paper? The repository is divided into 6 sections in the order of **data_collection**, **netsize_evaluation**, **ensemble_construction**, **PCA_ICA**, **node_interpretation**, **medium_analysis**. Each section provides a shell script that guides the analysis workflow. #### Python * tested on version 2.7.6 and 2.7.9 * Python packages will be installed automatically in the shell script * required packages: theano, docopt, requests, statsmodels, numpy #### R * tested on version 3.2.1 and 3.2.3 * R libraries are handled by the library [pacman](https://github.com/trinker/pacman), please install it first. * the following libraries will be installed/loaded when necessary by pacman: affy, affyio, [TDM](https://github.com/greenelab/TDM), doParallel, readr, ggplot2, gplots, sprint, ff, cluster, plyr, dendextend, gdata, limma ## How should I build a new eADAGE model? By modifying the *platform* and *organism* parameters in the **data_collection/ data_collection.sh** file, you can build an expression compendium for a new organism (if the organism uses that one major array platform.). Then you can follow the instructions in **eADAGE_construction.sh** to build an eADAGE model for it. ### Contact info Jie Tan (jie.tan.gr@dartmouth.edu)