GraphAlignment: GraphAlignment
Version 1.40.0

Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006))

Browse man pages Browse package API and functions Browse package files

AuthorJoern P. Meier <mail@ionflux.org>, Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg.
Bioconductor views GraphAndNetwork Network
Date of publicationNone
MaintainerJoern P. Meier <mail@ionflux.org>
Licensefile LICENSE
Version1.40.0
URL http://www.thp.uni-koeln.de/~berg/GraphAlignment/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GraphAlignment")

Man pages

AlignedPairs: Get aligned node pairs
AlignNetworks: Align networks
AnalyzeAlignment: Analyze an alignment
ComputeLinkParameters: Compute link parameters
ComputeM: Compute score matrix M
ComputeNodeParameters: Compute node parameters
ComputeScores: Compute scores
CreateScoreMatrix: Create score matrix
EncodeDirectedGraph: Encode directed graph
GenerateExample: Generate example input data
GetBinNumber: Get bin number
InitialAlignment: Create initial alignment
InvertPermutation: Invert permutation
LinearAssignment: Solve linear assignment problem
MatrixToBin: Convert matrix to bin representation
Permute: Permute rows and columns of a matrix
Trace: Calculate trace of a matrix
VectorToBin: Convert vector to bin representation

Functions

AlignNetworks Man page Source code
AlignedPairs Man page Source code
AnalyzeAlignment Man page Source code
ComputeLinkParameters Man page Source code
ComputeM Man page Source code
ComputeNodeParameters Man page Source code
ComputeScores Man page Source code
CreateScoreMatrix Man page Source code
EncodeDirectedGraph Man page Source code
GenerateExample Man page Source code
GetBinNumber Man page Source code
InitialAlignment Man page Source code
InvertPermutation Man page Source code
LinearAssignment Man page Source code
MatrixToBin Man page Source code
Permute Man page Source code
Trace Man page Source code
VectorToBin Man page Source code
ast.lib Source code
onAttach Source code
onLoad Source code
onUnload Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/GraphAlignment.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/GraphAlignment.R
inst/doc/GraphAlignment.Rnw
inst/doc/GraphAlignment.pdf
man
man/AlignNetworks.Rd
man/AlignedPairs.Rd
man/AnalyzeAlignment.Rd
man/ComputeLinkParameters.Rd
man/ComputeM.Rd
man/ComputeNodeParameters.Rd
man/ComputeScores.Rd
man/CreateScoreMatrix.Rd
man/EncodeDirectedGraph.Rd
man/GenerateExample.Rd
man/GetBinNumber.Rd
man/InitialAlignment.Rd
man/InvertPermutation.Rd
man/LinearAssignment.Rd
man/MatrixToBin.Rd
man/Permute.Rd
man/Trace.Rd
man/VectorToBin.Rd
src
src/GA_alloc.c
src/GA_alloc.h
src/GA_matrix.c
src/GA_matrix.h
src/GA_matrix_R.c
src/GA_matrix_R.h
src/GA_message.c
src/GA_message.h
src/GA_vector.c
src/GA_vector.h
src/GA_vector_R.c
src/GA_vector_R.h
src/GraphAlignment.c
src/GraphAlignment.h
src/gnrl.h
src/lap.c
src/lap.h
vignettes
vignettes/GraphAlignment.Rnw
vignettes/a.pdf
vignettes/align_principle2b1.pdf
vignettes/align_principle2c1.pdf
vignettes/align_principle_short1.pdf
vignettes/binning-01a.pdf
GraphAlignment documentation built on May 20, 2017, 9:41 p.m.