AdjacencyMatrix2Pathway
                        Function to coerce an adjacency matrix to a
                        pathway
Clipper                 Function to use clipper method on microarray or
                        RNA-Seq data
DEGraph                 Function to use DEGraph method on microarray or
                        RNA-Seq data
PWEA                    Function to use PWEA method on microarray or
                        RNA-Seq data
SPIA                    Function to use SPIA method on microarray or
                        RNA-Seq data
TAPPA                   Function to use TAPPA method on microarray or
                        RNA-Seq data
TBS                     Function to use TBS method on microarray or
                        RNA-Seq data
ToPASeq-package         Package for topology-based pathway analysis of
                        microarray and RNASeq data
TopologyGSA             Function to use TopologyGSA method on
                        microarray or RNA-Seq data
convertIdentifiersByVector
                        Function to convert identifiers in pathways by
                        user specified vector
defaultEdgeAttrs        Auxiliary data needed for SPIA method
graphNEL2Pathway        Function to coerce a graphNEL to a pathway
reduceGraph             Function to reduce the pathway graph
res                     Function to extract parts of object
