Package: CePa 0.8.0

Zuguang Gu

CePa: Centrality-Based Pathway Enrichment

This package 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. <https://doi.org/10.1093/bioinformatics/btt008>.

Authors:Zuguang Gu

CePa_0.8.0.tar.gz
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CePa.pdf |CePa.html✨
CePa/json (API)

Peer review:

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

On CRAN:

27 exports 2 stars 3.50 score 14 dependencies 22 mentions 60 scripts 376 downloads

Last updated 3 years agofrom:aa200b70a2. Checks:OK: 7. Indexed: yes.

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:BiocGenericsclicpp11gluegraphigraphlatticelifecyclemagrittrMatrixpkgconfigRgraphvizrlangvctrs