R: Virtual Inference of Protein-activity by Enriched Regulon analysis

# Virtual Inference of Protein-activity by Enriched Regulon analysis

## Documentation for package ‘viper’ version 1.46.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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
aREA | analytic Rank-based Enrichment Analysis
as.dist.signatureDistance | Distance matrix from signatureDistance objects
bootstrapmsviper | msviper bootstraps integration
bootstrapTtest | Bootstrapped signature by t-test
bootstrapTtest-method | Bootstrapped signature by t-test
bootstrapViper | bootstrapsViper
comNames | Combinatorial annotation
distMode | Mode of continuous distributions
fcvarna | Variance of columns for arrays with NA values
filterColMatrix | Filter for columns of a matrix with no loss of col and row names
filterCV | Coefficient of variation filter
filterCV-method | Coefficient of variation filter
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
rowTtest-method | 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
signatureDistance | Signature Distance
signatureDistance-class | signatureDistance
sigT | Sigmoid transformation
summary.msviper | List msviper results
ttestNull | Null model by sample permutation testing
ttestNull-method | 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
viperSignature-method | Generic S4 method for signature and sample-permutation null model for VIPER
viperSimilarity | VIPER similarity