RNAi                    Molecular phenotypes from single and double
                        knockdowns in RNAi screen
computeSmallWorldness   Compute smallworldness of a graph
computeSurvivalPValueForGenePairSet.output
                        Survival analysis for pairs of genes
computeSurvivalPValueGenePairAll.output
                        Survival analysis for pairs of genes (with
                        matched individuals)
computeSurvivalPValueOneGenePair
                        Survival analysis for one pair of genes
computeSurvivalPValueOneGenePair.output
                        Write results from survival analysis to output
                        for one pair of genes
constructDesignMatrix   Generate a design matrix from raw RNAi data.
mutations               Genetic mutation data in patients.
processDataMutSurv      Find matched individuals in mutation and
                        survival data
survival                Patient survival data.
testMutationalPatternAll.wrapper
                        Compute the p and q values of all pairwise gene
                        mutation patterns
tested_pairs            Gene pairs tested in the double knockdown
                        assay.
