CePa: Centrality-based pathway enrichment

Use pathway topology information to assign weight to pathway nodes.

AuthorZuguang Gu
Date of publication2012-09-11 08:35:47
MaintainerZuguang Gu <jokergoo@gmail.com>
LicenseGPL (>= 2)
Version0.5
http://mcube.nju.edu.cn/jokergoo/

View on CRAN

Man pages

cepa: Apply CePa algorithm on a single pathway

cepa.all: Apply CePa algorithm on a list of pathways under multiple...

cepa.all.parallel: use CePa package through parallel computing

cepa.ora: Apply centrality-extended ORA on a single pathway

cepa.ora.all: Apply centrality-extented ORA on a list of pathways

CePa-package: Centrality-based pathway enrichment

cepa.univariate: Apply centrality-extended GSA on a single pathway

cepa.univariate.all: Apply centrality-extented GSA on a list of pathways

gene.list: Differential gene list and background gene list

generate.pathway: Generate igraph object from edge list

get.cepa: get single cepa object from cepa.all object

pathway.nodes: names of the pathway nodes

PID.db: pathway catalogues from Pathway Interaction Database(PID)

plot.cepa: Plot the cepa object

plot.cepa.all: plot the cepa.all object

plotGraph: Plot graph for the pathway network

plotNull: Plot the null distribution of the pathway score

plot.pathway.catalogue: plot pathway.catalogue object

print.cepa: print the cepa object

print.cepa.all: print the cepa.all object

print.pathway.catalogue: print pathway.catalogue object

p.table: Table of p-values of pathways

radiality: Calculate radiality centrality

reach: Calculate largest reach centrality

read.cls: Read CLS format file

read.gct: Read GCT format file

report: Generate report for CePa analysis

sampleLabel: Generate data structure of sample labels

set.pathway.catalogue: store pathway data and pre-processing

spread: Calculate spread centrality

Files in this package

CePa
CePa/MD5
CePa/vignettes
CePa/vignettes/ref.bib
CePa/vignettes/pathway-part.PNG
CePa/vignettes/parsing-PID-pathway-data.Rnw
CePa/vignettes/p53pathway.pdf
CePa/vignettes/p53-null.pdf
CePa/vignettes/molecule-part.PNG
CePa/vignettes/levels.pdf
CePa/vignettes/interaction-part.PNG
CePa/vignettes/fdr.pdf
CePa/vignettes/f9.pdf
CePa/vignettes/f8.pdf
CePa/vignettes/f6.pdf
CePa/vignettes/f5.pdf
CePa/vignettes/f4.pdf
CePa/vignettes/f3.pdf
CePa/vignettes/f2.pdf
CePa/vignettes/f12.pdf
CePa/vignettes/f11.pdf
CePa/vignettes/f10.pdf
CePa/vignettes/f1.pdf
CePa/vignettes/CePa.Rnw
CePa/vignettes/bibliography.bib
CePa/vignettes/analysis-p53.Rnw
CePa/R
CePa/R/univariate_extension.R CePa/R/report.R CePa/R/read.gct.R CePa/R/read.cls.R CePa/R/plot_print.R CePa/R/pathway.nodes.R CePa/R/p.table.R CePa/R/ora_extension.R CePa/R/label.R CePa/R/global_variable.R CePa/R/get.cepa.R CePa/R/generate.pathway.R CePa/R/cepa.all.R CePa/R/cepa.all.parallel.R CePa/R/centrality.R
CePa/NAMESPACE
CePa/man
CePa/man/spread.Rd CePa/man/set.pathway.catalogue.Rd CePa/man/sampleLabel.Rd CePa/man/report.Rd CePa/man/read.gct.Rd CePa/man/read.cls.Rd CePa/man/reach.Rd CePa/man/radiality.Rd CePa/man/print.pathway.catalogue.Rd CePa/man/print.cepa.Rd CePa/man/print.cepa.all.Rd CePa/man/plotNull.Rd CePa/man/plotGraph.Rd CePa/man/plot.pathway.catalogue.Rd CePa/man/plot.cepa.Rd CePa/man/plot.cepa.all.Rd CePa/man/PID.db.Rd CePa/man/pathway.nodes.Rd CePa/man/p.table.Rd CePa/man/get.cepa.Rd CePa/man/generate.pathway.Rd CePa/man/gene.list.Rd CePa/man/cepa.univariate.Rd CePa/man/cepa.univariate.all.Rd CePa/man/cepa.Rd CePa/man/cepa.ora.Rd CePa/man/cepa.ora.all.Rd CePa/man/cepa.all.Rd CePa/man/cepa.all.parallel.Rd CePa/man/CePa-package.Rd
CePa/inst
CePa/inst/extdata
CePa/inst/extdata/swf
CePa/inst/extdata/swf/playerProductInstall.swf
CePa/inst/extdata/swf/CytoscapeWeb.swf
CePa/inst/extdata/js
CePa/inst/extdata/js/main.js
CePa/inst/extdata/js/json2.min.js
CePa/inst/extdata/js/cytoscapeweb.min.js
CePa/inst/extdata/js/AC_OETags.min.js
CePa/inst/extdata/cepa.template
CePa/inst/extdata/bk.genome
CePa/inst/doc
CePa/inst/doc/parsing-PID-pathway-data.Rnw
CePa/inst/doc/parsing-PID-pathway-data.pdf
CePa/inst/doc/CePa.Rnw
CePa/inst/doc/CePa.pdf
CePa/inst/doc/analysis-p53.Rnw
CePa/inst/doc/analysis-p53.pdf
CePa/DESCRIPTION
CePa/data
CePa/data/PID.db.rda
CePa/data/gene.list.rda
CePa/data/datalist
CePa/CHANGES

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