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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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Maintainer


  • person_outline Ulrich Bodenhofer

Publication for Affinity Propagation Clustering

APCluster citations

 (24)
library_books

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti

2018
PLoS Genet
PMCID: 5929573
PMID: 29672509
DOI: 10.1371/journal.pgen.1007357

[…] transformed gei scores (), using the mclust function of the mclust package in r []. clusters were then refined through the use of the affinity propagation statistical approach, implemented in the apcluster function of the apcluster package of r []. genes with gei scores significantly different between conditions were determined through clustering of the log transformed fold changes […]

library_books

A bibliometric analysis of natural language processing in medical research

2018
BMC Med Inform Decis Mak
PMCID: 5872501
PMID: 29589569
DOI: 10.1186/s12911-018-0594-x

[…] as k-means [], spectral clustering [] and super-paramagnetic clustering []. it identifies clusters with lower error rate and lower time consumption []., we performed ap clustering using an r package apcluster [] with a key terms correlation matrix as input data. the matrix was generated based on the co-occurrence matrix using ochiai correlation coefficient calculated […]

call_split

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
call_split See protocol

[…] replications., 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, […]

library_books

Combating subclonal evolution of resistant cancer phenotypes

2017
Nat Commun
PMCID: 5666005
PMID: 29093439
DOI: 10.1038/s41467-017-01174-3

[…] estimated based on cna., we started with diploid, missense snvs identified from deep wes by mutect for patient #1 to corroborate wgs-based subclone findings. these variants were then subjected to affinity propagation clustering (via r package apclust (https://cran.r-project.org/web/packages/apcluster/citation.html)), with similarity calculated via expsimmat(r = 2, w = 0.1), to identify groups […]

library_books

Comparing structural and transcriptional drug networks reveals signatures of drug activity and toxicity in transcriptional responses

2017
NPJ Syst Biol Appl
PMCID: 5572457
PMID: 28861278
DOI: 10.1038/s41540-017-0022-3

[…] edges) (supplementary fig. ). in order to visualize and extract useful information from the sdn, we identified communities via the ap clustering algorithm, as implemented in the r package apcluster (v. 1.3.5)., a community is defined as a group of nodes densely interconnected with each other and with fewer connections to nodes outside the group. each community was coded […]

library_books

Combining affinity propagation clustering and mutual information network to investigate key genes in fibroid

2017
PMCID: 5488419
PMID: 28672922
DOI: 10.3892/etm.2017.4481

[…] clusters and wk represented the within-cluster sum of squared errors. the clusters that met a threshold of gene numbers <50 were regarded as kl clusters., an ap clustering method included in the apcluster package version 1.3.2 (johannes kepler university, linz, austria) identifies an exemplar for each cluster, which was most representative for this cluster. it regards each data point […]


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

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