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 |
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 |
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 |