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 |
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