RamiGO: AmiGO visualize R interface

R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Author
Markus Schroeder, Daniel Gusenleitner, John Quackenbush, Aedin Culhane, Benjamin Haibe-Kains
Date of publication
None
Maintainer
Markus Schroeder <markus.schroeder@ucdconnect.ie>
License
Artistic-2.0
Version
1.20.0

View on Bioconductor

Man pages

adjM2gml
Create GML file from readAmigoDot output.
AmigoDot
AmigoDot constructor and accessors
AmigoDot-class
Class "AmigoDot"
AmigoDot.to.Cyto
Opening the AmigoDot graph in Cytoscape through RCytoscape.
AmigoDot.to.graphAM
Converts an AmigoDot S4 object to a graphAM object.
AmigoDot.to.graphNEL
Converts an AmigoDot S4 object to a graphNEL object.
c5.go.mapping
MSigDB C5 GO term to GO ID mapping
exportCytoGML
Writes out an igraph graph to a Cytoscape readable GML file.
getAmigoTree
Getting the DAG GO tree for a set of GO ID's.
igraph-class
Class '"igraph"'
RamiGO-package
AmiGO visualize R interface
readAmigoDot
Parser for the GraphViz DOT format.

Files in this package

RamiGO/.BBSoptions
RamiGO/DESCRIPTION
RamiGO/NAMESPACE
RamiGO/NEWS
RamiGO/R
RamiGO/R/AmigoDot-Class.R
RamiGO/R/AmigoDot.to.Cyto.R
RamiGO/R/AmigoDot.to.graphAM.R
RamiGO/R/AmigoDot.to.graphNEL.R
RamiGO/R/adjM2gml.R
RamiGO/R/exportCytoGML.R
RamiGO/R/getAmigoTree.R
RamiGO/R/readAmigoDot.R
RamiGO/build
RamiGO/build/RamiGO.pdf
RamiGO/build/vignette.rds
RamiGO/data
RamiGO/data/c5.go.mapping.rda
RamiGO/inst
RamiGO/inst/CITATION
RamiGO/inst/doc
RamiGO/inst/doc/RamiGO.R
RamiGO/inst/doc/RamiGO.Rnw
RamiGO/inst/doc/RamiGO.pdf
RamiGO/man
RamiGO/man/AmigoDot-class.Rd
RamiGO/man/AmigoDot.Rd
RamiGO/man/AmigoDot.to.Cyto.Rd
RamiGO/man/AmigoDot.to.graphAM.Rd
RamiGO/man/AmigoDot.to.graphNEL.Rd
RamiGO/man/RamiGO-package.Rd
RamiGO/man/adjM2gml.Rd
RamiGO/man/c5.go.mapping.Rd
RamiGO/man/exportCytoGML.Rd
RamiGO/man/getAmigoTree.Rd
RamiGO/man/igraph-class.Rd
RamiGO/man/readAmigoDot.Rd
RamiGO/vignettes
RamiGO/vignettes/RamiGO.Rnw
RamiGO/vignettes/cyto.png