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graphite (version 1.14.1)

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

1.14.1

License

AGPL-3

Maintainer

Gabriele Sales

Last Published

February 15th, 2017

Functions in graphite (1.14.1)

convertIdentifiers

Convert the node identifiers of a pathway.
pathways

Retrieve a list of pathways.
biocarta

BioCarta pathways
Pathways-class

Class "Pathways"
as.list.DeprecatedPathwayList

Convertion of DeprecatedPathwayLists into lists.
as.list.PathwayList

Convertion of PathwayLists into lists.
runSPIA

Run SPIA analysis
runTopologyGSA

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

Humancyc pathways
kegg

KEGG pathways
pathwayGraph

Graph representing the topology of a pathway
PathwayList-class

Class "PathwayList"
runDEGraph

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

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

Panther pathways
nci

NCI pathways
Pathway-class

Class "Pathway"
pathwayDatabases

List the available pathway databases.
runTopologyGSAMulti

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

Prepare pathway dataset needed by runSPIA.
reactome

Reactome pathways
cytoscapePlot

Plot a pathway graph in Cytoscape
DeprecatedPathwayList-class

Class "DeprecatedPathwayList"
runClipper

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

Run a topological analysis on an expression dataset using clipper.