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graphite (version 1.16.0)

GRAPH Interaction from pathway Topological Environment

Description

Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, Reactome and SPIKE databases.

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Version

Monthly Downloads

3

Version

1.16.0

License

AGPL-3

Maintainer

Gabriele Sales

Last Published

February 15th, 2017

Functions in graphite (1.16.0)

nci

NCI pathways
panther

Panther pathways
Pathways-class

Class "Pathways"
pathways

Retrieve a list of pathways.
kegg

KEGG pathways
humancyc

Humancyc pathways
runClipper

Run a topological analysis on an expression dataset using clipper.
runClipperMulti

Run a topological analysis on an expression dataset using clipper.
runDEGraph

Run a topological analysis on an expression dataset using DEGraph package.
runDEGraphMulti

Run a topological analysis on an expression dataset using DEGraph package.
as.list.DeprecatedPathwayList

Convertion of DeprecatedPathwayLists into lists.
as.list.PathwayList

Convertion of PathwayLists into lists.
reactome

Reactome pathways
prepareSPIA

Prepare pathway dataset needed by runSPIA.
biocarta

BioCarta pathways
convertIdentifiers

Convert the node identifiers of a pathway.
PathwayList-class

Class "PathwayList"
runSPIA

Run SPIA analysis
runTopologyGSA

Run a topological analysis on an expression dataset using topologyGSA.
pathwayGraph

Graph representing the topology of a pathway
cytoscapePlot

Plot a pathway graph in Cytoscape
Pathway-class

Class "Pathway"
DeprecatedPathwayList-class

Class "DeprecatedPathwayList"
pathwayDatabases

List the available pathway databases.
runTopologyGSAMulti

Run a topological analysis on an expression dataset using topologyGSA.