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graphite (version 1.12.0)

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

9

Version

1.12.0

License

AGPL-3

Maintainer

Gabriele Sales

Last Published

February 15th, 2017

Functions in graphite (1.12.0)

kegg

KEGG pathways
runTopologyGSAMulti

Run topological analyses on an expression dataset, calling topologyGSA over all the pathways in a list.
nci

NCI pathways
runTopologyGSA

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

Graph representing the topology of a pathway
prepareSPIA

Prepare pathway dataset needed by runSPIA.
convertIdentifiers

Convert the node identifiers of a pathway.
biocarta

BioCarta pathways
reactome

Reactome pathways
runClipper

Run a topological analysis on an expression dataset using the clipper.
cytoscapePlot

Plot a pathway graph in Cytoscape
runClipperMulti

Run topological analyses on an expression dataset, calling clipper over all the pathways in a list.
humancyc

Humancyc pathways
runDEGraph

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

Panther pathways
pathway-class

Class "pathway"
runSPIA

Run SPIA analysis
runDEGraphMulti

Run topological analyses on an expression dataset, calling DEGraph over all the pathways in a list.
spike

SPIKE pathways