clSamp                  Cluster samples by pathway over-representation
colPermIPL              Collect Inferred Pathway Levels (IPLs) from
                        PARADIGM runs on permuted data
colRealIPL              Collect Inferred Pathway Levels (IPLs) from
                        PARADIGM runs on real data
conMtf                  Find consensus pathway motifs from a list of
                        pathways
fltByPerm               Filter IPLs from real data by distribution from
                        permuted data
getSignifOvrOnCl        Get significantly over-represented gene sets
                        for clustered samples
ovrGMT                  Calculate over-representation of gene sets in
                        each sample by genes from sample's largest
                        sub-pathway
pltConMtf               Plot consensus pathway submodules
pltMtfPrtIPL            Plot a heatmap of IPLs on proteins from
                        consensus pathway submodules
pltNeiStt               Plot a heatmap of pathway and omic states of a
                        protein and its pathway neighbors
pltOvrHm                Plot a heatmap of over-represented gene sets
                        for clustered samples
pltSttKM                Plot a Kaplan-Meier curve for samples
                        stratified by given protein(s)' pathway states
ppCnInp                 Prepare input copy-number (CN) alteration data
                        to run PARADIGM
ppPermInp               Permute input genomic state data between genes
                        in the same sample
ppRealInp               Prepare input copy-number (CN) alteration and
                        RNA data to run PARADIGM
ppRnaInp                Prepare input RNA data to run PARADIGM
ppRunPrd                Prepare required files to run PARADIGM
runPermPrd              Run PARADIGM on permuted data
runPrd                  Run PARADIGM on multi-omic data
subNtw                  Subset pathways by IPL results
