CePa: Centrality-based pathway enrichment

Use pathway topology information to assign weight to pathway nodes.

Install the latest version of this package by entering the following in R:
install.packages("CePa")
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

Functions

cepa Man page
CePa Man page
cepa.all Man page
cepa.all.parallel Man page
cepa.ora Man page
cepa.ora.all Man page
CePa-package Man page
cepa.univariate Man page
cepa.univariate.all Man page
gene.list Man page
generate.pathway Man page
get.cepa Man page
pathway.catalogue Man page
pathway.nodes Man page
PID.db Man page
plot.cepa Man page
plot.cepa.all Man page
plotGraph Man page
plotNull Man page
plot.pathway.catalogue Man page
print.cepa Man page
print.cepa.all Man page
print.pathway.catalogue Man page
p.table Man page
radiality Man page
reach Man page
read.cls Man page
read.gct Man page
report Man page
sampleLabel Man page
set.pathway.catalogue Man page
spread Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.