aREA                    analytic Rank-based Enrichment Analysis
aecdf                   Approximate empirical commulative distribution
                        function
approxk2d               approxk2d
aracne2regulon          Regulon object generation from ARACNe results
aracne2regulon4cnv      Regulon object generation from ARACNe results
                        corrected by cnv
as.dist.signatureDistance
                        Distance matrix from signatureDistance objects
bootstrapTtest          Bootstrapped signature by t-test
bootstrapViper          bootstrapsViper
bootstrapmsviper        msviper bootstraps integration
comNames                Combinatorial annotation
distMode                Mode of continuous distributions
fcvarna                 Variance of columns for arrays with NA values
filterCV                Coefficient of variation filter
filterColMatrix         Filter for columns of a matrix with no loss of
                        col and row names
filterRowMatrix         Filter for rows of a matrix with no loss of col
                        and row names
frcv                    Coeficient of variations for rows
frvarna                 Variance of rows for arrays with NA values
groupPwea3              Proportionally Weighted Enrichment Analysis for
                        gene-set groups
integrateSignatures     Integrate signatures
ledge                   Leading-edge analysis
loadExpset              Loading expression sets
msviper                 msVIPER
msviper-class           The msviper class
msviperAnnot            msVIPER annotation change
msviperClass            msVIPER class
msviperCombinatorial    msviper combinatorial analysis
msviperSynergy          msviper synergy analysis
plot.msviper            Plot msviper results
pruneRegulon            Prune Regulons
pwea3NULLf              Null model function
pwea3NULLgroups         Regulon-specific NULL model
regulon-class           The regulon class
rowTtest                Student's t-test for rows
scale.signatureDistance
                        Scaling of signatureDistance objects
scaleGroups             Signatures with grouping variable
shadow                  Shadow analysis for msviper objects
shadowRegulon           Correction for pleiotropy
sigT                    Sigmoid transformation
signatureDistance       Signature Distance
signatureDistance-class
                        signatureDistance
summary.msviper         List msviper results
ttestNull               Null model by sample permutation testing
viper                   VIPER
viperRPT                viperRPT
viperSignature          Generic S4 method for signature and
                        sample-permutation null model for VIPER
viperSignature-class    viperSignature
viperSimilarity         VIPER similarity
