GeneExpressionSignature: Gene Expression Signature based Similarity Metric
Version 1.22.0

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.

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
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneExpressionSignature")

Popular man pages

exampleSet: sample data, a subset of the C-MAP
GeneExpressionSignature: Introduction to the GeneExpressionSignature Package
getRLs: Convert gene expression profiles to a ranked list (data...
RankMerging: Merging the ranker lists with the same labels of the...
ScoreGSEA: Compute pairwise distances between samples with method in...
ScorePGSEA: Compute pairwise distances between samples with method in...
SignatureDistance: Compute pairwise distances comprehensively.
See all...

All man pages Function index File listing

Man pages

exampleSet: sample data, a subset of the C-MAP
GeneExpressionSignature: Introduction to the GeneExpressionSignature Package
getRLs: Convert gene expression profiles to a ranked list (data...
RankMerging: Merging the ranker lists with the same labels of the...
ScoreGSEA: Compute pairwise distances between samples with method in...
ScorePGSEA: Compute pairwise distances between samples with method in...
SignatureDistance: Compute pairwise distances comprehensively.

Functions

FootruleMatrix Source code
GeneExpressionSignature Man page
RankMerging Man page Source code
ScoreGSEA Man page Source code
ScorePGSEA Man page Source code
SignatureDistance Man page Source code
exampleSet Man page
getRLs Man page Source code
integratePRL Source code
krubor Source code
quickenrichmentscore Source code

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
GeneExpressionSignature documentation built on May 20, 2017, 11:02 p.m.

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