Software
Below are selected software tools for some of the methods we have recently developed. Please visit my GitHub repo for more information and additional software.
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R-package netgsa for Network Based Gene Set Analysis
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R-package: grangerTlasso (Graphical Granger Causality using Truncating Lasso)
Note 1: This is an early test release of the package, and is intended for experimental use only.
The R-package glmnet should be installed in order for this package to work.
Note 2: The grangerTlasso package is no longer maintained and is replaced with the ngc package (Network Granger Causality), which implements multiple related methods and is available on GitHub.
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R-package: spacejam (Graph Estimation with Joint Additive Models)
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R-package: lassoscore (High-Dimensional Inference with the Penalized Score Test)
Please send any
comments and feedback to ashojaie {AT} uw {DOT} edu.