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.

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
http://www.bioinf.jku.at/software/apcluster/

View on CRAN

Functions

aggexcluster Man page
aggExCluster Man page
aggExCluster,character,ANY-method Man page
aggExCluster,function,ANY-method Man page
aggExCluster,matrix,ExClust-method Man page
aggExCluster,Matrix,ExClust-method Man page
aggExCluster,matrix,missing-method Man page
aggExCluster,Matrix,missing-method Man page
aggExCluster-methods Man page
aggExCluster,missing,ExClust-method Man page
aggexresult Man page
AggExResult Man page
AggExResult-class Man page
[[,AggExResult,index,missing-method Man page
[,AggExResult,index,missing,missing-method Man page
apcluster Man page
apcluster,character,ANY-method Man page
apclusterDemo Man page
apcluster-deprecated Man page
apcluster,dgTMatrix,missing-method Man page
apcluster,function,ANY-method Man page
apclusterK Man page
apclusterK,character,ANY-method Man page
apclusterK,dgTMatrix,missing-method Man page
apclusterK,function,ANY-method Man page
apclusterK,matrix,missing-method Man page
apclusterK,Matrix,missing-method Man page
apclusterK-methods Man page
apclusterK,sparseMatrix,missing-method Man page
apclusterL Man page
apclusterL,character,ANY-method Man page
apclusterL,function,ANY-method Man page
apclusterL,matrix,missing-method Man page
apclusterL-methods Man page
apcluster,matrix,missing-method Man page
apcluster,Matrix,missing-method Man page
apcluster-methods Man page
apcluster-package Man page
apcluster,sparseMatrix,missing-method Man page
apresult Man page
APResult Man page
APResult-class Man page
[[,APResult,index,missing-method Man page
[,APResult,index,missing,missing-method Man page
as.dendrogram Man page
as.dendrogram,AggExResult-method Man page
as.dendrogram,ExClust-method Man page
as.DenseSimilarityMatrix Man page
as.DenseSimilarityMatrix,matrix-method Man page
as.DenseSimilarityMatrix,Matrix-method Man page
as.DenseSimilarityMatrix-method Man page
as.DenseSimilarityMatrix,sparseMatrix-method Man page
as.hclust Man page
as.hclust,AggExResult-method Man page
as.hclust,ExClust-method Man page
as.SparseSimilarityMatrix Man page
as.SparseSimilarityMatrix,matrix-method Man page
as.SparseSimilarityMatrix,Matrix-method Man page
as.SparseSimilarityMatrix-methods Man page
as.SparseSimilarityMatrix,sparseMatrix-method Man page
ch22Promoters Man page
conversions Man page
corSimMat Man page
cutree Man page
cutree,AggExResult-method Man page
cutree,APResult-method Man page
cutree-methods Man page
exclust Man page
ExClust Man page
ExClust-class Man page
[[,ExClust,index,missing-method Man page
[,ExClust,index,missing,missing-method Man page
expSimMat Man page
heatmap Man page
heatmap,AggExResult,matrix-method Man page
heatmap,AggExResult,missing-method Man page
heatmap,ExClust,matrix-method Man page
heatmap,ExClust,Matrix-method Man page
heatmap,ExClust,missing-method Man page
heatmap,ExClust,sparseMatrix-method Man page
heatmap,matrix,missing-method Man page
heatmap-methods Man page
heatmap,missing,matrix-method Man page
labels Man page
labels,APResult-method Man page
labels,ExClust-method Man page
labels-methods Man page
length,AggExResult-method Man page
length,APResult-method Man page
length,ExClust-method Man page
linKernel Man page
linSimMat Man page
negDistMat Man page
plot Man page
plot,AggExResult,data.frame-method Man page
plot,AggExResult,matrix-method Man page
plot,AggExResult,missing-method Man page
plot,APResult,missing-method Man page
plot,ExClust,data.frame-method Man page
plot,ExClust,matrix-method Man page
plot,ExClust,missing-method Man page
plot-methods Man page
preferenceRange Man page
preferenceRange,dgTMatrix-method Man page
preferenceRange,matrix-method Man page
preferenceRange,Matrix-method Man page
preferenceRange-methods Man page
preferenceRange,sparseMatrix-method Man page
show Man page
show,AggExResult-method Man page
show,APResult-method Man page
show,ExClust-method Man page
show-methods Man page
similarities Man page
similarity Man page
similarity,AggExResult-method Man page
similarity,APResult-method Man page
similarity,ExClust-method Man page
sort Man page
sort,APResult-method Man page
sort,ExClust-method Man page
sort-methods Man page
sparseToFull Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.