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mixtools specifications

Information


Unique identifier OMICS_29449
Name mixtools
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 1.1.0
Stability Stable
Requirements
stats, MASS, survival, R(≥3.2.0), segmented
Source code URL https://cran.r-project.org/src/contrib/mixtools_1.1.0.tar.gz
Maintained Yes

Subtool


  • normalmixEM

Versioning


No version available

Documentation


Publication for mixtools

mixtools citations

 (52)
library_books

Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing end tracking protein

2018
PLoS Genet
PMCID: 5944918
PMID: 29746462
DOI: 10.1371/journal.pgen.1007221

[…] termine their depolymerization rates based on the angles formed. To estimate the mean velocities for fast and slow depolymerizing ends we used a two Gaussians mixture model from the mixtools package (normalmixEM procedure) from R (RStudio), which is based on the iterative expectation maximization (EM) algorithm. […]

library_books

Multi omics profiling of younger Asian breast cancers reveals distinctive molecular signatures

2018
Nat Commun
PMCID: 5928087
PMID: 29713003
DOI: 10.1038/s41467-018-04129-4

[…] and -positive samples have expression values drawn from two Gaussian distributions with their respective mean and standard deviations. Using an expectation maximization (EM) method implemented by the mixtools package in R, we assigned probabilities of being drawn from either distribution to each sample with measured expression levels. Proportion of receptor positive/negative samples as measured by […]

library_books

Comparative Heterochromatin Profiling Reveals Conserved and Unique Epigenome Signatures Linked to Adaptation and Development of Malaria Parasites

2018
PMCID: 5853956
PMID: 29503181
DOI: 10.1016/j.chom.2018.01.008

[…] ompartment. To do so, we fitted a bivariate Gaussian mixture model to the data and calculated the probabilities (p) for genes to belong to either one of the two compartments using the modelling tool ‘normalmixEM‘ from the R package ‘mixtools’. For further analysis genes with p > 0.99999 for the ‘heterochromatic’ compartment were considered high confidence heterochromatic genes. Genes with 0.99999  […]

library_books

Large scale profiling of noncoding RNA function in yeast

2018
PLoS Genet
PMCID: 5864082
PMID: 29529031
DOI: 10.1371/journal.pgen.1007253

[…] d normal distribution on the dataset and used the standard EM algorithm to determine means and standard deviations from the mixture of strains with normal growth and others with reduced fitness using Mixtools []. The P values were calculated from the parameters that are closer to the wild-type and fitness differences considered significant with p < 0.05. […]

call_split

An information theoretic approach to the modeling and analysis of whole genome bisulfite sequencing data

2018
BMC Bioinformatics
PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5
call_split See protocol

[…] ) can then be used to model and compute the desired null distribution.To build this mixture model, we transform the sJSD values using the logit function logit(x)=logx1−x.We then employ the R package mixtools to estimate a mixture of two Gaussian distributions that best fits the empirical distribution of the observed logit-transformed sJSD values using the EM algorithm. This produces the means μ1, […]

library_books

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse

2018
Front Genet
PMCID: 5807349
PMID: 29459883
DOI: 10.3389/fgene.2018.00026

[…] e (), which is based upon the concept of a quantile–quantile plot extended to n dimensions. To check that the data distribution conforms to the same type of distribution after normalization, we used ‘mixtools’ (). Second, we used the Power Law Global Error Model (PLGEM) () to detect differentially expressed/abundant proteins using the functions plgem.fit and plgem-stn (). Due to similar statistica […]

Citations

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mixtools institution(s)
Pennsylvania State University, State College, PA, USA; Universite d’Orleans, Orleans, France
mixtools funding source(s)
Supported by NSF Award SES-0518772, and Le Studium, an agency of the Centre National de la Recherche Scientifique of France.

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