CePa-package            Centrality-based pathway enrichment
PID.db                  pathway catalogues from Pathway Interaction
                        Database(PID)
cepa                    Apply CePa algorithm on a single pathway
cepa.all                Apply CePa algorithm on a list of pathways
                        under multiple centralities
cepa.all.parallel       use CePa package through parallel computing
cepa.ora                Apply centrality-extended ORA on a single
                        pathway
cepa.ora.all            Apply centrality-extented ORA on a list of
                        pathways
cepa.univariate         Apply centrality-extended GSA on a single
                        pathway
cepa.univariate.all     Apply centrality-extented GSA on a list of
                        pathways
gene.list               Differential gene list and background gene list
generate.pathway        Generate igraph object from edge list
get.cepa                get single cepa object from cepa.all object
p.table                 Table of p-values of pathways
pathway.nodes           names of the pathway nodes
plot.cepa               Plot the cepa object
plot.cepa.all           plot the cepa.all object
plot.pathway.catalogue
                        plot pathway.catalogue object
plotGraph               Plot graph for the pathway network
plotNull                Plot the null distribution of the pathway score
print.cepa              print the cepa object
print.cepa.all          print the cepa.all object
print.pathway.catalogue
                        print pathway.catalogue object
radiality               Calculate radiality centrality
reach                   Calculate largest reach centrality
read.cls                Read CLS file which stores the phenotype data
read.gct                Read GCT format file which stores the
                        expression values
report                  Generate report for CePa analysis
sampleLabel             Generate data structure of sample labels
set.pathway.catalogue   store pathway data and pre-processing
spread                  Calculate radiality centrality
