viper: Virtual Inference of Protein-activity by Enriched Regulon analysis
Version 1.10.0

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

AuthorMariano J Alvarez <reef103@gmail.com>
Bioconductor views FunctionalPrediction GeneExpression GeneRegulation NetworkEnrichment SystemsBiology
Date of publicationNone
MaintainerMariano J Alvarez <reef103@gmail.com>
Licensefile LICENSE
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("viper")

Popular man pages

aracne2regulon: Regulon object generation from ARACNe results
aracne2regulon4cnv: Regulon object generation from ARACNe results corrected by...
aREA: analytic Rank-based Enrichment Analysis
as.dist.signatureDistance: Distance matrix from signatureDistance objects
bootstrapTtest-methods: Bootstrapped signature by t-test
summary.msviper: List msviper results
viper: VIPER
See all...

All man pages Function index File listing

Man 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...
aREA: analytic Rank-based Enrichment Analysis
as.dist.signatureDistance: Distance matrix from signatureDistance objects
bootstrapmsviper: msviper bootstraps integration
bootstrapTtest-methods: 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...
filterCV-methods: 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...
integrateSignatures: Integrate signatures
ledge: Leading-edge analysis
loadExpset: Loading expression sets
msviper: msVIPER
msviperAnnot: msVIPER annotation change
msviper-class: The msviper class
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-methods: Student's t-test for rows
scaleGroups: Signatures with grouping variable
scale.signatureDistance: Scaling of signatureDistance objects
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-methods: Null model by sample permutation testing
viper: VIPER
viperRPT: viperRPT
viperSignature-class: viperSignature
viperSignature-methods: Generic S4 method for signature and sample-permutation null...
viperSimilarity: VIPER similarity

Functions

TFmode1 Source code
TFmode2 Source code
TFscore Source code
aREA Man page Source code
aecdf Man page Source code
aecdf1 Source code
approxk2d Man page Source code
aracne2regulon Man page Source code
aracne2regulon4cnv Man page Source code
as.dist.signatureDistance Man page Source code
bootstrapTtest Man page
bootstrapTtest,ExpressionSet-method Man page
bootstrapTtest,matrix-method Man page
bootstrapViper Man page Source code
bootstrapmsviper Man page Source code
comNames Man page Source code
comregulationAnalysis Source code
distMode Man page Source code
fcvarna Man page Source code
filterCV Man page
filterCV,ExpressionSet-method Man page
filterCV,matrix-method Man page
filterColMatrix Man page Source code
filterRowMatrix Man page Source code
frcv Man page Source code
frvarna Man page Source code
groupPwea3 Man page Source code
gsea2ESint Source code
integrateSignatures Man page Source code
ledge Man page Source code
loadExpset Man page Source code
msviper Man page Source code
msviper-class Man page
msviperAnnot Man page Source code
msviperClass Man page Source code
msviperCombinatorial Man page Source code
msviperSynergy Man page Source code
plot.msviper Man page Source code
ppwea3NULLf Source code
print.msviper Source code
print.regulon Source code
pruneRegulon Man page Source code
pwea3NULLf Man page Source code
pwea3NULLgroups Man page Source code
readAracneAdj Source code
regulon-class Man page
regulonDist Source code
regulonScore Source code
rowTtest Man page
rowTtest,ExpressionSet-method Man page
rowTtest,matrix-method Man page
rowVars Source code
scale.signatureDistance Man page Source code
scaleGroups Man page Source code
selectTFs Source code
shadow Man page Source code
shadowRegulon Man page Source code
sigT Man page Source code
signatureDistance Man page Source code
signatureDistance-class Man page
summary.msviper Man page Source code
summary.regulon Source code
ttestNull Man page
ttestNull,ExpressionSet-method Man page
ttestNull,matrix-method Man page
updateRegulon Source code
viper Man page Source code
viperRPT Man page Source code
viperSignature Man page
viperSignature,ExpressionSet-method Man page
viperSignature,matrix-method Man page
viperSignature-class Man page
viperSimilarity Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/aracne.r
R/clases.r
R/general.r
R/internal.r
R/ledge.r
R/msviper.r
R/plot.r
R/rpt.r
R/shadow.r
R/signatureDistance.r
R/viper.r
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/viper.R
inst/doc/viper.Rnw
inst/doc/viper.pdf
man
man/aREA.Rd
man/aecdf.Rd
man/approxk2d.Rd
man/aracne2regulon.Rd
man/aracne2regulon4cnv.Rd
man/as.dist.signatureDistance.Rd
man/bootstrapTtest-methods.Rd
man/bootstrapViper.Rd
man/bootstrapmsviper.Rd
man/comNames.Rd
man/distMode.Rd
man/fcvarna.Rd
man/filterCV-methods.Rd
man/filterColMatrix.Rd
man/filterRowMatrix.Rd
man/frcv.Rd
man/frvarna.Rd
man/groupPwea3.Rd
man/integrateSignatures.Rd
man/ledge.Rd
man/loadExpset.Rd
man/msviper-class.Rd
man/msviper.Rd
man/msviperAnnot.Rd
man/msviperClass.Rd
man/msviperCombinatorial.Rd
man/msviperSynergy.Rd
man/plot.msviper.Rd
man/pruneRegulon.Rd
man/pwea3NULLf.Rd
man/pwea3NULLgroups.Rd
man/regulon-class.Rd
man/rowTtest-methods.Rd
man/scale.signatureDistance.Rd
man/scaleGroups.Rd
man/shadow.Rd
man/shadowRegulon.Rd
man/sigT.Rd
man/signatureDistance-class.Rd
man/signatureDistance.Rd
man/summary.msviper.Rd
man/ttestNull-methods.Rd
man/viper.Rd
man/viperRPT.Rd
man/viperSignature-class.Rd
man/viperSignature-methods.Rd
man/viperSimilarity.Rd
vignettes
vignettes/viper.Rnw
viper documentation built on May 20, 2017, 10:22 p.m.