DeltaNet is a network analysis tool for predicting genetic perturbations from gene expression data. Given a compendium of gene expression data, DeltaNet generates a perturbation score for each gene in every sample. For a given sample, the magnitude of a gene perturbation scores reflects the confidence that this gene is directly perturbed (for example, by drug or chemical compounds), while the sign reflects the nature of the perturbation (positive for gene induction, negative for gene repression).
Two versions of DeltaNet are available; DeltaNet-LAR which uses least angle regression and DeltaNet-LASSO which uses LASSO regression. The subroutines in the DeltaNet package (v.1.0) have been successfully tested on MATLAB® 2014b and 2015a platforms. The subroutines in the DeltaNetR package have been successfully tested on R versions 3.2.2 and 3.2.3. Please refer to our manuscript titled “Inferring gene targets of drugs and chemical compounds from gene expression profiles” for more detailed information about DeltaNet algorithm.
DeltaNet: MATLAB® software (version R2014b or later) and SpaSM package (last version on 24.10.2012) and GLMNET package
DeltaNet-R: R software (versions 3.2.2 or 3.2.3 ) and R packages: "lars" for DeltaNet-lar, "glmnet", "cvTools" and "methods" for DeltaNet-lasso, and "doParallel" and "foreach" for parallel computing.
DeltaNet: 17.02.2016
DeltaNet-R: 27.06.2016
Redistribution and use in source and binary forms, with or without modification, are permitted provided agreeing to the Simplified BSD Style License (see more).
License (RTF, 2 KB)
DeltaNet (MATLAB version): Download and unzip the DeltaNet.zip file.
The information on how to install and use DeltaNet can be found in the README for MATLAB.
DeltaNet-R (R version): Download and unzip the DeltaNetR.zip file.
The information on how to install and use DeltaNet-R can be found in the README for R.
This work has been supported by the ETH Zurich Research Grant. We would like to thank S.M. Minhaz Ud-Dean for providing useful suggestions and for supporting the computing environment and maintenance.