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Transcriptional regulatory network inference from gene expression and prior information with LASSO-StARS

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infTRN_lassoStARS

This repository contains a workflow for inference of transcriptional regulatory networks (TRNs) from gene expression data and prior information, as described in:

Miraldi et al., Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.

From gene expression data and tables of prior information, the example Th17 workflow can be used to infer a TRN using modified LASSO-StARS, and relies upon GlmNet in MATLAB to solve the LASSO. Workflow also includes TRN model evaluation based on precision-recall and ROC.

The resulting network can be visualized with TRN visualization software: jp_gene_viz.

Additional workflows are provided for:

NOTE: For Mac users of MATLAB 2016b or later versions, you might need to install gfortran. We recommend the following: Install Homebrew, and then install gfortran with the Terminal command: "brew cask install gfortran".

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Transcriptional regulatory network inference from gene expression and prior information with LASSO-StARS

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