APCluster statistics

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Citations per year

Number of citations per year for the bioinformatics software tool APCluster
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Tool usage distribution map

This map represents all the scientific publications referring to APCluster per scientific context
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Associated diseases

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Protocols

APCluster specifications

Information


Unique identifier OMICS_14867
Name APCluster
Alternative name Affinity Propagation Clustering
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.4.7
Stability Stable
Requirements
methods, stats, graphics, Matrix, Biostrings, grDevices, knitr, R(≥3.0.0), Rcpp(≥0.11.1), kebabs(≥1.5.4)
Maintained Yes

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Documentation


Maintainer


  • person_outline Ulrich Bodenhofer

Publication for Affinity Propagation Clustering

APCluster citations

 (11)
library_books

Defining objective clusters for rabies virus sequences using affinity propagation clustering

2018
PLoS Negl Trop Dis
PMCID: 5794188
PMID: 29357361
DOI: 10.1371/journal.pntd.0006182

[…] Pairwise distances as calculated in the phylogenetic analysis were merged into a distance matrix and imported to the statistical software R []. For further analyses the package “apcluster” was used essentially as described []. By default, the AP clustering algorithm determines one sequence among the set of input elements for each potential cluster, which is most representativ […]

library_books

Gut metagenomes of type 2 diabetic patients have characteristic single nucleotide polymorphism distribution in Bacteroides coprocola

2017
Microbiome
PMCID: 5286682
PMID: 28143583
DOI: 10.1186/s40168-017-0232-3

[…] ed to the matrix. The hclust function of stat package in R v3.3.0 was used for hierarchical clustering with parameters “method = complete,” and the output tree was drawn by ggtree. For AP clustering, APcluster in R v3.3.0 was employed with parameters “K = 2.” The clusters generated by AP clustering were visualized by using Cytoscape v3.5.0 []. For each node, the top five edges connecting the nodes […]

library_books

Discrimination of Picea chihuahuana Martinez populations on the basis of climatic, edaphic, dendrometric, genetic and population traits

2017
PeerJ
PMCID: 5470581
PMID: 28626616
DOI: 10.7717/peerj.3452

[…] ables, nine genetic and species diversity variables, 10 dasometric variables, four density variables, T and dmin (–).All analyses were implemented using the R Script for k-Means Cluster Analysis and “apcluster” software packages () executed in the R free statistical application ().The AP and k-means clustering techniques recommended only two clusters of P. chihuahuana populations under study, whic […]

library_books

Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate Producing, Clostridial Scavenger from Metagenomic Sequence Data

2016
Front Microbiol
PMCID: 4880562
PMID: 27303377
DOI: 10.3389/fmicb.2016.00783

[…] was computed using FastTree () with the parameters -nt -gtr -gamma -slownni -spr 4 -mlacc 2. The ANIb phylogeny was computed by using JSpecies () and then performing hierarchical clustering using the apcluster package. The tetranucleotide whole-genome phylogeny was constructed by computing the canonical tetranucleotide spectra of all genomes (), transforming these data into z-scores and calculatin […]

library_books

Forest Owners' Response to Climate Change: University Education Trumps Value Profile

2016
PLoS One
PMCID: 4880312
PMID: 27223473
DOI: 10.1371/journal.pone.0155137

[…] value strengths, the individuals’ loadings on the identified clusters of values were used to cluster private forest owners for each country into groups representing different value profiles using the Affinity Propagation Clustering methodology [] (, and ). The data for each country were analyzed separately so as not to make any assumptions about the cross-national validity of the value profiles i […]

library_books

A genome‐scale screen reveals context‐dependent ovarian cancer sensitivity to miRNA overexpression

2015
Mol Syst Biol
PMCID: 4704493
PMID: 26655797
DOI: 10.15252/msb.20156308

[…] Clustering analysis was performed with the affinity propagation clustering (APC) algorithm using the “apcluster” package in R. APC is a deterministic clustering method which identifies the number of clusters, and cluster “exemplars” (i.e., the cluster centroid or the data point that is the best repres […]


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APCluster institution(s)
Institute of Bioinformatics, Johannes Kepler University, Linz, Austria

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