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mixOmics specifications

Information


Unique identifier OMICS_12504
Name mixOmics
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 6.3.0
Stability Stable
Requirements
MASS, lattice, ggplot2
Source code URL https://cran.r-project.org/web/packages/mixOmics/index.html
Maintained No

Subtools


  • DIABLO (Data Integration Analysis for Biomark
  • MINT
  • MixMC
  • PLS DA
  • sPLS-DA (Sparse Partial Least-Squares Discrim

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Publications for mixOmics

mixOmics in pipelines

 (6)
2017
PMCID: 5649194
PMID: 29085340
DOI: 10.3389/fmicb.2017.01806

[…] and the data have been deposited in the gene expression omnibus (geo) database (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse78759), under the accession number gse103392., the package mixomics employs partial least square (pls) based methods to unravel relationships between variables from multiple biological datasets. the tool has its own tutorial and can be easily used, […]

2016
PMCID: 4740858
PMID: 26843130
DOI: 10.1038/srep20318

[…] to be differentially expressed. partial least squares discriminant analysis (pls-da) of genes showing the greatest variation in expression (top 5% coefficient of variation) was performed using the mixomics package (version 5.0-1) for r. over-representation analysis of differentially expressed genes were performed using the cluego application (version 2.1.1) in cytoscape (version 3.1). […]

2015
PMCID: 4446756
PMID: 26007332
DOI: 10.3390/nu7053370

[…] over-represented. partial least squares-discriminant analysis (pls-da) was performed on genes that showed the highest variation across all samples (top 5% coefficient of variation) using the mixomics package [] in r. pls-da is a multivariate analysis that is commonly used for classification purposes by maximising the explained variance between groups. it is an appropriate choice […]

2015
PMCID: 4518884
PMID: 26220188
DOI: 10.1186/s12864-015-1733-8

[…] the use of a quadratic regression analysis (masigpro r package). in addition, we studied the behaviour of the microbiota over time and looked for correlations with gene expression patterns using the mixomics r package, because it is known that the microbiota and gut mucosal tissue respond to each other in various ways [, ]., for analysis of data derived from three time-points and two treatments, […]

2014
PMCID: 4078401
PMID: 24991220
DOI: 10.1186/1710-1492-10-32

[…] using the linear models for microarrays (limma) r-library []. the benjamini-hochberg false discovery rate (fdr) was used to correct for multiple testing. partial least squares (pls), from the mixomics r-library [] was used to identify the relationship between cell-specific gene lists. statistical analyses were performed in the statistical computing program r version 3.0.1 []., to test […]


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mixOmics in publications

 (135)
PMCID: 5943556
PMID: 29774016
DOI: 10.3389/fmicb.2018.00869

[…] (r foundation for statistical computing, ). to test for a correlation between taxonomical and functional composition, a canonical correlation analysis using the cca (gonzález et al., ) and mixomics (rohart et al., ) packages in r were applied. with cca, the function-taxon cross-correlation was computed by maximizing the linear combinations between the two matrix vectors. […]

PMCID: 5928086
PMID: 29712900
DOI: 10.1038/s41467-018-03906-5

[…] filtering, had become fixed after 300 generations, and were within protein-coding regions, were used for the downstream statistical analyses implemented in r using the packages vegan (2.4–3), mixomics (6.1–3), ade4 (1.7–10), topgo (2.26–0, with bioconductor 3.4), biomart (2.3–0 with bioconductor 3.4), and phangorn (2.2–0)., the matrices were first used for pcas based on euclidean distance […]

PMCID: 5923279
PMID: 29703927
DOI: 10.1038/s41598-018-24978-9

[…] component of the variables in both data sets. from these matrices, relevance networks, inferred from pairwise association scores between x and y variables, were built using the network function of mixomics to reveal correlation structures between the metabolites and the de traits. these networks included 32 variables for the ileal content, 28 for the caecal content, and 15 for the serum […]

PMCID: 5925865
PMID: 29755604
DOI: 10.2174/1874285801812010071

[…] was determined using nmds with the bray-curtis distance method. sparse partial least squares discriminant analysis (s pls da) was performed to determine the most discriminant otu using the mixomics package [] with css normalization and log transformation of count sequences. a cutoff value of 0.95 was used to select the discriminant otus. statistical analyses were performed with anova […]

PMCID: 5914196
PMID: 29719546
DOI: 10.3389/fpls.2018.00485

[…] metabolites in different kegg pathways with an mbrole fdr correction of less than 0.05. multivariate analysis of metabolites and physiological parameters (supplementary table ) were conducted with mixomics () using principal component analysis (pca), sparse partial least squares (spls), and network analyses. the normalization of the datasets was performed before combining them. spls algorithm […]


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mixOmics institution(s)
Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville, Castanet-Tolosan, France; Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, UPS, Toulouse, France
mixOmics funding source(s)
Supported by the French Laboratory of Excellence project "TULIP" (ANR-10-LABX-41; ANR-11-IDEX-0002-02), and the Midi-Pyrénées Region and the Federal University of Toulouse.

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