mclust protocols

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chevron_left Gene expression clustering Gene expression classification chevron_right
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mclust specifications

Information


Unique identifier OMICS_27435
Name mclust
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 5.4
Stability Stable
Source code URL https://cran.r-project.org/web/packages/mclust/index.html
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Luca Scrucca <>
  • person_outline Michael Fop <>
  • person_outline Brendan Murphy <>
  • person_outline Adrian Raftery <>

Additional information


https://www.stat.washington.edu/raftery/Research/PDF/fraley1999.pdf

Publication for mclust

mclust in pipelines

 (15)
2017
PMCID: 5318454
PMID: 28270818
DOI: 10.3389/fpls.2017.00166

[…] archive as of january 1st, 2017, under the following accession number: srp081139., clustering of transcript expression patterns across the five time-points for nil175 and nil163 was performed using mclust v5.0.1 (www.stat.washington.edu/mclust/) in r64 v3.2.0 (www.r-project.org/). mclust uses a mixed method that combines model-based hierarchical clustering, em for gaussian mixture models, […]

2017
PMCID: 5613027
PMID: 28947812
DOI: 10.1038/s41598-017-12510-4

[…] 0.05 between any compared stages. genes with a pcc value less than −0.85 were used in clustering analysis. dmr genes at each methylation context were grouped and clustered separately. the r package mclust (https://www.r-project.org) was used to determine the model-based optimal number of clusters to use. the log2-transfromed expression levels in fpkm were loaded into cluster 3; the expression […]

2017
PMCID: 5640240
PMID: 29028833
DOI: 10.1371/journal.ppat.1006668

[…] standardized across all 15 samples by mean-centering and scaling so that standard deviations are all set to 1. genes were then clustered using model-based clustering as implemented in the r package mclust. an average profile was created for each gene cluster by taking the mean over the standardized expression values for all the genes in the cluster. next, the average profiles were merged using […]

2017
PMCID: 5688804
PMID: 29115931
DOI: 10.1186/s12885-017-3726-2

[…] previously [, ]. briefly, for each gene, log2 + 1-transformed [], upper quartile-normalized [] gene expression was fitted for a 2-component gaussian mixture distribution model with the r package mclust []. the highest match between the assignment and clinical data (when available) was the criterion for selecting equal or variable variance between the two gaussian fits. for the microarray […]

2017
PMCID: 5729917
PMID: 29208119
DOI: 10.1099/mgen.0.000140

[…] false discovery rate (fdr), the benjamini–hochberg method was used, which computes an upper bound for the expected fdr and adjusts the p value accordingly to correct for multiple testing []. the r mclust package [] was used to perform bimodal clustering of genes to either a ‘reduced’ or ‘unchanged’ mode, by fitting a parameterized bimodal gaussian mixture model to the log2-transformed fold […]


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mclust in publications

 (361)
PMCID: 5942782
PMID: 29742166
DOI: 10.1371/journal.pone.0195286

[…] and the sign of component loadings is arbitrary (can be positive or negative depending on the algorithm or data used)., farms were clustered using gaussian mixture model-based clustering with the mclust package in r [,]. in this method data are considered to originate from a distribution that is a combination of two or more components (i.e. clusters). each component is modelled by a gaussian […]

PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] kilobase per million mapped reads) values, we aggregated the log2(fpkm) values per group (g02–g06) and fitted a one-dimensional normal mixture model with two components and variable variance with mclust [] to each group separately. after obtaining classification vectors, the midpoint between the maximum log2(fpkm) value of the legs and the minimum log2(fpkm) value of the hegs was considered. […]

PMCID: 5923235
PMID: 29703992
DOI: 10.1038/s41467-018-03727-6

[…] (b) the fret acceptor intensity of doubly labelled, fret capable, monomeric protein (control 1); and (c) the direct donor excitation of monomeric singly labelled receptor (control 2), using the mclust package for r. to account for differences in sample size between the intensity distributions for the three data sets, the data were bootstrapped 1000 times, taking random samples of n = 1000 […]

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

[…] 3.2.3 and log transformed. initial clustering of the data was performed through the fitting of an optimal number of overlapping guassian distributions to the log 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 […]

PMCID: 5889077
PMID: 29624590
DOI: 10.1371/journal.pone.0195084

[…] we performed two multivariate analyses that do not require a priori groupings: principal component analysis (pca) and an unsupervised model-based clustering using gaussian mixtures analysis via mclust 5.0.2 package [,]. in addition, we performed a discriminant analysis through eigenvalue decomposition [] and the misclassification rate of the pre-established morphogroups was assessed […]


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mclust institution(s)
Università degli Studi di Perugia, Perugia, Italy; University College Dublin, Dublin, Ireland; University of Washington, Seattle, WA, USA
mclust funding source(s)
Supported by the Science Foundation Ireland funded Insight Research Centre (SFI/12/RC/2289) and NIH grants R01 HD054511, R01 HD070936 and U54 HL127624.

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