Package: viper 1.47.0

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]>

viper_1.47.0.tar.gz
viper_1.47.0.zip(r-4.7)viper_1.47.0.zip(r-4.6)viper_1.47.0.zip(r-4.5)
viper_1.47.0.tgz(r-4.6-any)viper_1.47.0.tgz(r-4.5-any)
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viper_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
viper/json (API)

# Install 'viper' in R:

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

On BioConductor:viper-1.47.0(bioc 3.24)viper-1.46.0(bioc 3.23)

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

systemsbiology networkenrichment geneexpression functionalprediction generegulation

7.12 score 5 packages 484 scripts 9 mentions 30 exports 78 dependencies

Last updated from:5e67590fd0. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	176
linux-devel-x86_64	WARNING	320
source / vignettes	OK	331
linux-release-x86_64	WARNING	262
macos-release-arm64	WARNING	155
macos-oldrel-arm64	WARNING	163
windows-devel	WARNING	229
windows-release	WARNING	223
windows-oldrel	WARNING	255
wasm-release	OK	161

Exports:approxk2d aracne2regulon aracne2regulon4cnv aREA bootstrapmsviper bootstrapTtest distMode fcvarna filterColMatrix filterCV filterRowMatrix frcv frvarna integrateSignatures ledge msviper msviperAnnot msviperClass msviperCombinatorial msviperSynergy pruneRegulon rowTtest scaleGroups shadow signatureDistance ttestNull viper viperRPT viperSignature viperSimilarity

Dependencies:askpass base64enc Biobase BiocGenerics bslib cachem class cli cpp11 crosstalk curl data.table digest dplyr e1071 evaluate farver fastmap fontawesome fs generics ggplot2 glue gtable highr htmltools htmlwidgets httr isoband jquerylib jsonlite kernlab KernSmooth knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mime mixtools nlme openssl otel pillar pkgconfig plotly promises proxy purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales segmented stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Using VIPER

Rendered fromviper.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Approximate empirical commulative distribution function	aecdf
approxk2d	approxk2d
Regulon object generation from ARACNe results	aracne2regulon
Regulon object generation from ARACNe results corrected by cnv	aracne2regulon4cnv
analytic Rank-based Enrichment Analysis	aREA
Distance matrix from signatureDistance objects	as.dist.signatureDistance
msviper bootstraps integration	bootstrapmsviper
Bootstrapped signature by t-test	bootstrapTtest bootstrapTtest,ExpressionSet-method bootstrapTtest,matrix-method
bootstrapsViper	bootstrapViper
Combinatorial annotation	comNames
Mode of continuous distributions	distMode
Variance of columns for arrays with NA values	fcvarna
Filter for columns of a matrix with no loss of col and row names	filterColMatrix
Coefficient of variation filter	filterCV filterCV,ExpressionSet-method filterCV,matrix-method
Filter for rows of a matrix with no loss of col and row names	filterRowMatrix
Coeficient of variations for rows	frcv
Variance of rows for arrays with NA values	frvarna
Proportionally Weighted Enrichment Analysis for gene-set groups	groupPwea3
Integrate signatures	integrateSignatures
Leading-edge analysis	ledge
Loading expression sets	loadExpset
msVIPER	msviper
The msviper class	msviper-class
msVIPER annotation change	msviperAnnot
msVIPER class	msviperClass
msviper combinatorial analysis	msviperCombinatorial
msviper synergy analysis	msviperSynergy
Plot msviper results	plot.msviper
Prune Regulons	pruneRegulon
Null model function	pwea3NULLf
Regulon-specific NULL model	pwea3NULLgroups
The regulon class	regulon-class
Student's t-test for rows	rowTtest rowTtest,ExpressionSet-method rowTtest,matrix-method
Scaling of signatureDistance objects	scale.signatureDistance
Signatures with grouping variable	scaleGroups
Shadow analysis for msviper objects	shadow
Correction for pleiotropy	shadowRegulon
Signature Distance	signatureDistance
signatureDistance	signatureDistance-class
Sigmoid transformation	sigT
List msviper results	summary.msviper
Null model by sample permutation testing	ttestNull ttestNull,ExpressionSet-method ttestNull,matrix-method
VIPER	viper
viperRPT	viperRPT
Generic S4 method for signature and sample-permutation null model for VIPER	viperSignature viperSignature,ExpressionSet-method viperSignature,matrix-method
viperSignature	viperSignature-class
VIPER similarity	viperSimilarity