GraphAlignment: GraphAlignment

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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))

Author
Joern P. Meier <mail@ionflux.org>, Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg.
Date of publication
None
Maintainer
Joern P. Meier <mail@ionflux.org>
License
file LICENSE
Version
1.38.0
URLs

View on Bioconductor

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

Files in this package

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