Signaling Pathway Impact Analysis (SPIA) is a standard Bioconductor style R package designed to perform pathway analysis using over representation evidence and pathway topology information.

The package is available directly from the Bioconductor website here.

Details about the method can be found in the reference below:

Other relevant references include:

  • Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R. A systems biology approach for pathway level analysis. Genome Res 2007;17(10):1537-45.
  • Khatri P, Draghici S, Tarca AL, Hassan SS, Romero R. A system biology approach for the steady-state analysis of gene signaling networks. Lecture Notes in Computer Science; 2007,32-41.