GeneExpressionSignature: Gene Expression Signature based Similarity Metric

This package gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneExpressionSignature")
AuthorYang Cao
Bioconductor views GeneExpression
Date of publicationNone
MaintainerYang Cao <yiluheihei@gmail.com>, Fei Li <pittacus@gmail.com>,Lu Han <hanl8910@gmail.com>
LicenseGPL-2
Version1.20.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/FootruleMatrix.R R/RankMerging.R R/ScoreGSEA.R R/ScorePGSEA.R R/SignatureDistance.R R/getRLs.R R/integratePRL.R R/krubor.R R/quickenrichmentscore.R
build
build/vignette.rds
data
data/datalist
data/exampleSet.rda
inst
inst/doc
inst/doc/GeneExpressionSignature.R
inst/doc/GeneExpressionSignature.Rnw
inst/doc/GeneExpressionSignature.pdf
inst/extdata
inst/extdata/GSM118720.soft
inst/extdata/GSM118721.soft
man
man/GeneExpressionSignature.Rd man/RankMerging.Rd man/ScoreGSEA.Rd man/ScorePGSEA.Rd man/SignatureDistance.Rd man/exampleSet.Rd man/getRLs.Rd
vignettes
vignettes/GeneExpressionSignature.Rnw
vignettes/GeneExpressionSignature.bib
vignettes/Thumbs.db
vignettes/cluster.png

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