apcluster: Affinity Propagation Clustering

Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) <DOI:10.1126/science.1136800>. 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.

Author
Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier
Date of publication
2016-02-24 10:18:34
Maintainer
Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
License
GPL (>= 2)
Version
1.4.3
URLs

View on CRAN

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

Files in this package

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