Package: CePa 0.8.1

Zuguang Gu

CePa: Centrality-Based Pathway Enrichment

It aims to find significant pathways through network topology information. It has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centrality measures are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system. CePa extends standard pathway enrichment methods, which include both over-representation analysis procedure and gene-set analysis procedure. <doi:10.1093/bioinformatics/btt008>.

Authors:Zuguang Gu [aut, cre]

CePa_0.8.1.tar.gz
CePa_0.8.1.tar.gz(r-4.5-noble)CePa_0.8.1.tar.gz(r-4.4-noble)
CePa_0.8.1.tgz(r-4.4-emscripten)CePa_0.8.1.tgz(r-4.3-emscripten)
CePa.pdf |CePa.html✨
CePa/json (API)

# Install 'CePa' in R:
install.packages('CePa', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jokergoo/cepa/issues

Datasets:
  • PID.db - Pathway catalogues from Pathway Interaction Database
  • gene.list - Differential gene list and background gene list

4.35 score 75 scripts 463 downloads 22 mentions 27 exports 15 dependencies

Last updated 2 months agofrom:a264c980a5. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 08 2024
R-4.5-linuxOKDec 08 2024

Exports:cepacepa.allcepa.all.parallelcepa.oracepa.ora.allcepa.univariatecepa.univariate.allgenerate.pathwayget.cepap.tablepathway.nodesplot.cepaplot.cepa.allplot.pathway.catalogueplotGraphplotNullprint.cepaprint.cepa.allprint.pathway.catalogueradialityreachread.clsread.gctreportsampleLabelset.pathway.cataloguespread

Dependencies:BiocGenericsclicpp11genericsgluegraphigraphlatticelifecyclemagrittrMatrixpkgconfigRgraphvizrlangvctrs

analysis-p53

Rendered fromanalysis-p53.Rnwusingutils::Sweaveon Dec 08 2024.

Last update: 2018-06-04
Started: 2012-09-05

CePa Vignette

Rendered fromCePa.Rnwusingutils::Sweaveon Dec 08 2024.

Last update: 2022-06-11
Started: 2012-04-20

parsing-PID

Rendered fromparsing-PID-pathway-data.Rnwusingutils::Sweaveon Dec 08 2024.

Last update: 2022-06-11
Started: 2012-09-05

Readme and manuals

Help Manual

Help pageTopics
Centrality-based pathway enrichmentCePa-package
Apply CePa algorithm on a single pathwaycepa
Apply CePa algorithm on a list of pathways under multiple centralitiescepa.all
use CePa package through parallel computingcepa.all.parallel
Apply centrality-extended ORA on a single pathwaycepa.ora
Apply centrality-extented ORA on a list of pathwayscepa.ora.all
Apply centrality-extended GSA on a single pathwaycepa.univariate
Apply centrality-extented GSA on a list of pathwayscepa.univariate.all
Differential gene list and background gene listgene.list
Generate igraph object from edge listgenerate.pathway
get single cepa object from cepa.all objectget.cepa
Table of p-values of pathwaysp.table
names of the pathway nodespathway.nodes
pathway catalogues from Pathway Interaction Database(PID)PID.db
Plot the cepa objectplot.cepa
plot the cepa.all objectplot.cepa.all
plot pathway.catalogue objectplot.pathway.catalogue
Plot graph for the pathway networkplotGraph
Plot the null distribution of the pathway scoreplotNull
print the cepa objectprint.cepa
print the cepa.all objectprint.cepa.all
print pathway.catalogue objectprint.pathway.catalogue
Calculate radiality centralityradiality
Calculate largest reach centralityreach
Read CLS file which stores the phenotype dataread.cls
Read GCT format file which stores the expression valuesread.gct
Generate report for CePa analysisreport
Generate data structure of sample labelssampleLabel
store pathway data and pre-processingset.pathway.catalogue
Calculate radiality centralityspread