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 |

http://www.thp.uni-koeln.de/~berg/GraphAlignment/ |

**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

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

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