CePa: Centrality-based pathway enrichment

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Use pathway topology information to assign weight to pathway nodes.

Author
Zuguang Gu
Date of publication
2012-09-11 08:35:47
Maintainer
Zuguang Gu <jokergoo@gmail.com>
License
GPL (>= 2)
Version
0.5
URLs

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