apcluster: Affinity Propagation Clustering
Version 1.4.3

Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) . The algorithms are largely analogous to the 'Matlab' code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.

AuthorUlrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier
Date of publication2016-02-24 10:18:34
MaintainerUlrich Bodenhofer <bodenhofer@bioinf.jku.at>
LicenseGPL (>= 2)
Version1.4.3
URL http://www.bioinf.jku.at/software/apcluster/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("apcluster")

Getting started

Package overview

Popular man pages

apclusterK-methods: Affinity Propagation for Pre-defined Number of Clusters
apclusterL-methods: Leveraged Affinity Propagation
apcluster-methods: Affinity Propagation
conversions: Conversions Between Dense and Sparse Similarity Matrices
preferenceRange-methods: Determine Meaningful Ranges for Input Preferences
show-methods: Display Clustering Result Objects
similarities: Methods for Computing Similarity Matrices
See all...

All man pages Function index File listing

Man pages

aggExCluster-methods: Exemplar-based Agglomerative Clustering
AggExResult-class: Class "AggExResult"
apclusterDemo: Affinity Propagation Demo
apcluster-deprecated: Deprecated functions in package 'apcluster'
apclusterK-methods: Affinity Propagation for Pre-defined Number of Clusters
apclusterL-methods: Leveraged Affinity Propagation
apcluster-methods: Affinity Propagation
apcluster-package: APCluster Package
APResult-class: Class "APResult"
ch22Promoters: ch22Promoters Data Set
coerce-methods: Coercion of cluster hierarchies
conversions: Conversions Between Dense and Sparse Similarity Matrices
cutree-methods: Cut Out Clustering Level from Cluster Hierarchy
ExClust-class: Class "ExClust"
heatmap-methods: Plot Heatmap
labels-methods: Generate label vector from clustering result
plot-methods: Plot Clustering Results
preferenceRange-methods: Determine Meaningful Ranges for Input Preferences
show-methods: Display Clustering Result Objects
similarities: Methods for Computing Similarity Matrices
sort-methods: Sort clusters

Functions

Files

TODO
inst
inst/examples
inst/examples/ch22Promoters.fasta
inst/CITATION
inst/doc
inst/doc/apcluster.R
inst/doc/apcluster.Rnw
inst/doc/apcluster.pdf
src
src/preferenceRangeC.cpp
src/preferenceRangeSparseC.cpp
src/apclusterC.cpp
src/apclusterLeveragedC.cpp
src/apclusterSparseC.cpp
src/distanceL.c
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/show-methods.R
R/apclusterK-methods.R
R/sort-methods.R
R/revDend.R
R/cutree-methods.R
R/apcluster-methods.R
R/heatmap-methods.R
R/simpleDist.R
R/labels-methods.R
R/access-methods.R
R/plot-methods.R
R/preferenceRange-methods.R
R/apclusterDemo.R
R/length-methods.R
R/aggExCluster-methods.R
R/similarity.R
R/coerce-methods.R
R/conversions.R
R/apclusterL-methods.R
vignettes
vignettes/bioinf-bar.png
vignettes/apcluster.Rnw
vignettes/bioinf-article.txi
vignettes/bioinf.cls
MD5
build
build/vignette.rds
DESCRIPTION
man
man/conversions.Rd
man/heatmap-methods.Rd
man/APResult-class.Rd
man/plot-methods.Rd
man/ExClust-class.Rd
man/apclusterL-methods.Rd
man/apclusterK-methods.Rd
man/AggExResult-class.Rd
man/sort-methods.Rd
man/ch22Promoters.Rd
man/apclusterDemo.Rd
man/labels-methods.Rd
man/apcluster-methods.Rd
man/cutree-methods.Rd
man/coerce-methods.Rd
man/aggExCluster-methods.Rd
man/similarities.Rd
man/apcluster-package.Rd
man/show-methods.Rd
man/apcluster-deprecated.Rd
man/preferenceRange-methods.Rd
apcluster documentation built on May 20, 2017, 2:10 a.m.

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