mclust pipeline

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: 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: 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 [55]. the r mclust package [56] 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 […]

2017
PMCID: 5912503
PMID: 28783152
DOI: 10.1038/ni.3799

[…] new matrix of methylation values including all replicates. we applied complete-linkage hierarchical clustering to generate a heatmap using r (v3.1.2) and pheatmap. we further applied r (v3.1.2) and mclust(v5.1)[1] to estimate the number of clusters using parameters: mclust(…, g=1:20). the resulting number of clusters was four and we cut the resulting tree for the dmrs from the complete-linkage […]

2017
PMCID: 5912503
PMID: 28783152
DOI: 10.1038/ni.3799

[…] complete-linkage hierarchical clustering to generate a heatmap using r (v3.1.2) and pheatmap. we further applied r (v3.1.2) and mclust(v5.1)[1] to estimate the number of clusters using parameters: mclust(…, g=1:20). the resulting number of clusters was four and we cut the resulting tree for the dmrs from the complete-linkage using cutree (…, k=4) into four different clusters., […]

2016
PMCID: 5042848
PMID: 27571262
DOI: 10.1038/ng.3650

[…] and esr1-negative tumours (supplementary figure 12). consistent with the metabric23 analysis, we determined the expression status of tcga tumours for esr1, pgr, and erbb2 among tcga samples using mclust in r. we fitted a gaussian finite mixture model with two components. we restricted the analysis to luminal-type tumours, those that express both esr1 and pgr, but do not overexpress erbb2. […]

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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