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. Author manuscript; available in PMC: 2017 Nov 1.
Published in final edited form as: Prog Retin Eye Res. 2016 Jun 11;55:1–31. doi: 10.1016/j.preteyeres.2016.06.001

Table 7.

Systems Integration Tools

Method Tool Availability
Network
Inference 		Integrative Inference Of
Regulatory Networks		 http://compbio.mit.edu/flynet/
Binding And Expression
Target Analysis (BETA)		 http://cistrome.org/BETA/
Integrated Regulatory
Network Framework		 Available upon request to authors.
Physical Module
Networks		 http://www.compbio.cs.huji.ac.il/PMN/Welcome.html
eQTL Matrix Eqtl https://cran.r-project.org/web/packages/MatrixEQTL/
Eqtl https://cran.r-project.org/web/packages/eqtl/
Genetictools https://cran.r-project.org/web/packages/GeneticTools/