Package: viper 1.41.0

Mariano J Alvarez

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

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

Authors:Mariano J Alvarez <[email protected]>

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viper.pdf |viper.html✨
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NEWS

# Install 'viper' in R:
install.packages('viper', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:viper-1.41.0(bioc 3.21)viper-1.40.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

systemsbiologynetworkenrichmentgeneexpressionfunctionalpredictiongeneregulation

7.00 score 5 packages 340 scripts 1.1k downloads 9 mentions 30 exports 80 dependencies

Last updated 2 months agofrom:6d8ed69f42. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 07 2024
R-4.5-winWARNINGDec 07 2024
R-4.5-linuxWARNINGDec 07 2024
R-4.4-winWARNINGDec 07 2024
R-4.4-macWARNINGDec 07 2024
R-4.3-winWARNINGDec 07 2024
R-4.3-macWARNINGDec 07 2024

Exports:approxk2daracne2regulonaracne2regulon4cnvaREAbootstrapmsviperbootstrapTtestdistModefcvarnafilterColMatrixfilterCVfilterRowMatrixfrcvfrvarnaintegrateSignaturesledgemsvipermsviperAnnotmsviperClassmsviperCombinatorialmsviperSynergypruneRegulonrowTtestscaleGroupsshadowsignatureDistancettestNullviperviperRPTviperSignatureviperSimilarity

Dependencies:askpassbase64encBiobaseBiocGenericsbslibcachemclassclicolorspacecpp11crosstalkcurldata.tabledigestdplyre1071evaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonlitekernlabKernSmoothknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemixtoolsmunsellnlmeopensslpillarpkgconfigplotlypromisesproxypurrrR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalessegmentedstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Using VIPER

Rendered fromviper.Rnwusingutils::Sweaveon Dec 07 2024.

Last update: 2019-02-26
Started: 2014-03-20

Readme and manuals

Help Manual

Help pageTopics
Approximate empirical commulative distribution functionaecdf
approxk2dapproxk2d
Regulon object generation from ARACNe resultsaracne2regulon
Regulon object generation from ARACNe results corrected by cnvaracne2regulon4cnv
analytic Rank-based Enrichment AnalysisaREA
Distance matrix from signatureDistance objectsas.dist.signatureDistance
msviper bootstraps integrationbootstrapmsviper
Bootstrapped signature by t-testbootstrapTtest bootstrapTtest,ExpressionSet-method bootstrapTtest,matrix-method
bootstrapsViperbootstrapViper
Combinatorial annotationcomNames
Mode of continuous distributionsdistMode
Variance of columns for arrays with NA valuesfcvarna
Filter for columns of a matrix with no loss of col and row namesfilterColMatrix
Coefficient of variation filterfilterCV filterCV,ExpressionSet-method filterCV,matrix-method
Filter for rows of a matrix with no loss of col and row namesfilterRowMatrix
Coeficient of variations for rowsfrcv
Variance of rows for arrays with NA valuesfrvarna
Proportionally Weighted Enrichment Analysis for gene-set groupsgroupPwea3
Integrate signaturesintegrateSignatures
Leading-edge analysisledge
Loading expression setsloadExpset
msVIPERmsviper
The msviper classmsviper-class
msVIPER annotation changemsviperAnnot
msVIPER classmsviperClass
msviper combinatorial analysismsviperCombinatorial
msviper synergy analysismsviperSynergy
Plot msviper resultsplot.msviper
Prune RegulonspruneRegulon
Null model functionpwea3NULLf
Regulon-specific NULL modelpwea3NULLgroups
The regulon classregulon-class
Student's t-test for rowsrowTtest rowTtest,ExpressionSet-method rowTtest,matrix-method
Scaling of signatureDistance objectsscale.signatureDistance
Signatures with grouping variablescaleGroups
Shadow analysis for msviper objectsshadow
Correction for pleiotropyshadowRegulon
Signature DistancesignatureDistance
signatureDistancesignatureDistance-class
Sigmoid transformationsigT
List msviper resultssummary.msviper
Null model by sample permutation testingttestNull ttestNull,ExpressionSet-method ttestNull,matrix-method
VIPERviper
viperRPTviperRPT
Generic S4 method for signature and sample-permutation null model for VIPERviperSignature viperSignature,ExpressionSet-method viperSignature,matrix-method
viperSignatureviperSignature-class
VIPER similarityviperSimilarity