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

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

AuthorMariano J Alvarez <reef103@gmail.com>
Date of publicationNone
MaintainerMariano J Alvarez <reef103@gmail.com>
Licensefile LICENSE
Version1.8.0

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

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