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

Functions

aecdf Man page
approxk2d Man page
aracne2regulon Man page
aracne2regulon4cnv Man page
aREA Man page
as.dist.signatureDistance Man page
bootstrapmsviper Man page
bootstrapTtest Man page
bootstrapTtest,ExpressionSet-method Man page
bootstrapTtest,matrix-method Man page
bootstrapViper Man page
comNames Man page
distMode Man page
fcvarna Man page
filterColMatrix Man page
filterCV Man page
filterCV,ExpressionSet-method Man page
filterCV,matrix-method Man page
filterRowMatrix Man page
frcv Man page
frvarna Man page
groupPwea3 Man page
integrateSignatures Man page
ledge Man page
loadExpset Man page
msviper Man page
msviperAnnot Man page
msviper-class Man page
msviperClass Man page
msviperCombinatorial Man page
msviperSynergy Man page
plot.msviper Man page
pruneRegulon Man page
pwea3NULLf Man page
pwea3NULLgroups Man page
regulon-class Man page
rowTtest Man page
rowTtest,ExpressionSet-method Man page
rowTtest,matrix-method Man page
scaleGroups Man page
scale.signatureDistance Man page
shadow Man page
shadowRegulon Man page
signatureDistance Man page
signatureDistance-class Man page
summary.msviper Man page
ttestNull Man page
ttestNull,ExpressionSet-method Man page
ttestNull,matrix-method Man page
viper Man page
viperRPT Man page
viperSignature Man page
viperSignature-class Man page
viperSignature,ExpressionSet-method Man page
viperSignature,matrix-method Man page
viperSimilarity Man page

Files

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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