Man pages for jokergoo/CePa
Centrality-Based Pathway Enrichment
| 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 file which stores the phenotype data |
| read.gct | Read GCT format file which stores the expression values |
| report | Generate report for CePa analysis |
| sampleLabel | Generate data structure of sample labels |
| set.pathway.catalogue | store pathway data and pre-processing |
| spread | Calculate radiality centrality |
