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CePa (version 0.7.0)
Centrality-Based Pathway Enrichment
Description
Use pathway topology information to assign weight to pathway nodes.
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Install
install.packages('CePa')
Monthly Downloads
324
Version
0.7.0
License
GPL (>= 2)
Issues
0
Pull Requests
0
Stars
2
Forks
3
Repository
https://github.com/jokergoo/CePa
Maintainer
Zuguang Gu
Last Published
February 25th, 2020
Functions in CePa (0.7.0)
Search functions
cepa.ora.all
Apply centrality-extented ORA on a list of pathways
CePa-package
Centrality-based pathway enrichment
cepa
Apply CePa algorithm on a single pathway
cepa.univariate
Apply centrality-extended GSA on a single pathway
PID.db
pathway catalogues from Pathway Interaction Database(PID)
cepa.ora
Apply centrality-extended ORA on a single pathway
cepa.all.parallel
use CePa package through parallel computing
cepa.all
Apply CePa algorithm on a list of pathways under multiple centralities
cepa.univariate.all
Apply centrality-extented GSA on a list of pathways
gene.list
Differential gene list and background gene list
plotNull
Plot the null distribution of the pathway score
generate.pathway
Generate igraph object from edge list
plot.pathway.catalogue
plot pathway.catalogue object
set.pathway.catalogue
store pathway data and pre-processing
spread
Calculate radiality centrality
plotGraph
Plot graph for the pathway network
radiality
Calculate radiality centrality
print.cepa
print the cepa object
reach
Calculate largest reach centrality
pathway.nodes
names of the pathway nodes
report
Generate report for CePa analysis
p.table
Table of p-values of pathways
plot.cepa.all
plot the cepa.all object
plot.cepa
Plot the cepa object
print.cepa.all
print the cepa.all object
get.cepa
get single cepa object from cepa.all object
read.cls
Read CLS file which stores the phenotype data
sampleLabel
Generate data structure of sample labels
read.gct
Read GCT format file which stores the expression values
print.pathway.catalogue
print pathway.catalogue object