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viper (version 1.6.0)

Virtual Inference of Protein-activity by Enriched Regulon analysis

Description

Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms

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Version

Version

1.6.0

License

GPL (>=2)

Maintainer

Mariano J Alvarez

Last Published

February 15th, 2017

Functions in viper (1.6.0)

approxk2d

approxk2d
loadExpset

Loading expression sets
viperSignature

Generic S4 method for signature and sample-permutation null model for VIPER
aracne2regulon

Regulon object generation from ARACNe results
as.dist.signatureDistance

Distance matrix from signatureDistance objects
frcv

Coeficient of variations for rows
msviperCombinatorial

msviper combinatorial analysis
viper

VIPER
scaleGroups

Signatures with grouping variable
msviperClass

msVIPER class
bootstrapViper

bootstrapsViper
comNames

Combinatorial annotation
shadowRegulon

Correction for pleiotropy
msviper-class

The msviper class
pwea3NULLgroups

Regulon-specific NULL model
msviperAnnot

msVIPER annotation change
aracne2regulon4cnv

Regulon object generation from ARACNe results corrected by cnv
summary.msviper

List msviper results
ttestNull

Null model by sample permutation testing
bootstrapTtest

Bootstrapped signature by t-test
frvarna

Variance of rows for arrays with NA values
regulon-class

The regulon class
rowTtest

Student's t-test for rows
pruneRegulon

Prune Regulons
pwea3NULLf

Null model function
viperSimilarity

VIPER similarity
fcvarna

Variance of columns for arrays with NA values
msviper

msVIPER
signatureDistance-class

signatureDistance
shadow

Shadow analysis for msviper objects
filterRowMatrix

Filter for rows of a matrix with no loss of col and row names
msviperSynergy

msviper synergy analysis
viperRPT

viperRPT
aecdf

Approximate empirical commulative distribution function
bootstrapmsviper

msviper bootstraps integration
filterCV

Coefficient of variation filter
groupPwea3

Proportionally Weighted Enrichment Analysis for gene-set groups
integrateSignatures

Integrate signatures
scale.signatureDistance

Scaling of signatureDistance objects
distMode

Mode of continuous distributions
filterColMatrix

Filter for columns of a matrix with no loss of col and row names
viperSignature-class

viperSignature
aREA

analytic Rank-based Enrichment Analysis
ledge

Leading-edge analysis
signatureDistance

Signature Distance
plot.msviper

Plot msviper results