| 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 |
| 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 |
| 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 |
| runPermPrd |
Run PARADIGM on permuted data |
| runPrd |
Run PARADIGM on multi-omic data |
| subNtw |
Subset pathways by IPL results |
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