RDocumentation
Moon
Learn R
Search all packages and functions
graphite (version 1.18.0)
GRAPH Interaction from pathway Topological Environment
Description
Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, Reactome and SPIKE databases.
Copy Link
Copy
Link to current version
Version
Version
1.18.0
1.16.0
1.14.1
1.12.0
Down Chevron
Monthly Downloads
22
Version
1.18.0
License
AGPL-3
Maintainer
Gabriele Sales
Last Published
May 3rd, 2016
Functions in graphite (1.18.0)
Search functions
cytoscapePlot
Plot a pathway graph in Cytoscape
convertIdentifiers
Convert the node identifiers of a pathway.
pathwayDatabases
List the available pathway databases.
pathwayGraph
Graph representing the topology of a pathway
pathways
Retrieve a list of pathways.
prepareSPIA
Prepare pathway dataset needed by runSPIA.
kegg
KEGG pathways
nci
NCI pathways
reactome
Reactome pathways
runClipper
Run a topological analysis on an expression dataset using clipper.
runDEGraphMulti
Run a topological analysis on an expression dataset using DEGraph package.
runSPIA
Run SPIA analysis
as.list.DeprecatedPathwayList
Convertion of DeprecatedPathwayLists into lists.
as.list.PathwayList
Convertion of PathwayLists into lists.
PathwayList-class
Class
"PathwayList"
Pathways-class
Class
"Pathways"
runDEGraph
Run a topological analysis on an expression dataset using DEGraph package.
runClipperMulti
Run a topological analysis on an expression dataset using clipper.
DeprecatedPathwayList-class
Class
"DeprecatedPathwayList"
humancyc
Humancyc pathways
panther
Panther pathways
Pathway-class
Class
"Pathway"
runTopologyGSAMulti
Run a topological analysis on an expression dataset using topologyGSA.
runTopologyGSA
Run a topological analysis on an expression dataset using topologyGSA.
biocarta
BioCarta pathways
buildPathway
Build a Pathway object.