Package: staRank 1.45.0

Juliane Siebourg

staRank: Stability Ranking

Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling.

Authors:Juliane Siebourg, Niko Beerenwinkel

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staRank.pdf |staRank.html✨
staRank/json (API)

# Install 'staRank' in R:

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

The latest version of this package failed to build. Look at thebuild logs for more information.

Datasets:

salmonellaInfection - RNAi screen of human cells during Salmonella infection
salmonellaStability - Example stability analysis on a subset of the Salmonella infection dataset

On BioConductor:staRank-1.47.0(bioc 3.20)staRank-1.46.0(bioc 3.19)

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

bioconductor-package

18 exports 0.82 score 82 dependencies

Last updated 9 months agofrom:7d1bd94c31

Exports:aggregRank avrgRank baseRank dataFormatRSA getRankmatrix getSampleScores getStability method mwTest2samp Pi rankCor RankSummary runRSA stabilityRanking stableSetSize stabRank summaryStats uniqueRSARanking

Dependencies:affy affyio annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem Category cellHTS2 cli colorspace cpp11 crayon curl DBI fansi farver fastmap genefilter GenomeInfoDb GenomeInfoDbData ggplot2 glue graph GSEABase gtable httr hwriter IRanges isoband jsonlite KEGGREST labeling lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png preprocessCore R6 RBGL RColorBrewer rlang RSQLite S4Vectors scales splots statmod survival sys tibble UCSC.utils utf8 vctrs viridisLite vsn withr XML xtable XVector zlibbioc

Using staRank

Rendered fromstaRank.Rnwusingutils::Sweaveon May 02 2024.

Last update: 2012-05-09
Started: 2012-05-09

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Stability ranking	staRank-package staRank
aggregRank	aggregRank
Get average ranking	avrgRank avrgRank,RankSummary-method
Get base ranking	baseRank baseRank,RankSummary-method
dataFormatRSA	dataFormatRSA
getRankmatrix	getRankmatrix
Get Sample Scores	getSampleScores getSampleScores,list-method getSampleScores,matrix-method
getStability	getStability
Get method	method method,RankSummary-method
mwTest2samp	mwTest2samp
Get Pi	Pi Pi,RankSummary-method
Get rank correlations	rankCor rankCor,RankSummary-method
Class RankSummary	RankSummary RankSummary-class
runRSA	runRSA
RNAi screen of human cells during Salmonella infection	salmonellaInfection
Example stability analysis on a subset of the Salmonella infection dataset	salmonellaStability
Show function for a RankSummary object.	show show,RankSummary-method
Wrapper to perform stabilityRanking	stabilityRanking stabilityRanking,cellHTS-method stabilityRanking,matrix-method stabilityRanking,numeric-method
Get stable set sizes	stableSetSize stableSetSize,RankSummary-method
Get stability ranking	stabRank stabRank,RankSummary-method
Summary method for RankSummary object	summary summary,RankSummary-method
Summary statistic per element	summaryStats summaryStats,list-method summaryStats,matrix-method
uniqueRSARanking	uniqueRSARanking