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

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

Author
Mariano J Alvarez <reef103@gmail.com>
Date of publication
None
Maintainer
Mariano J Alvarez <reef103@gmail.com>
License
file LICENSE
Version
1.8.0

View on Bioconductor

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
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

Files in this package

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