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Multivariate Data Integration Using R: Methods and Applications with the mixOmics Package

1st, 2021

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mixOmics: An R package for 'omics feature selection and multiple data integration

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005752-e1005752

2017

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DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays

Bioinformatics (Oxford, England), 2019-09, Vol.35 (17), p.3055-3062

2019

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Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems

BMC bioinformatics, 2011-06, Vol.12 (1), p.253-253, Article 253

2011

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Intestinal Metaproteomics Reveals Host-Microbiota Interactions in Subjects at Risk for Type 1 Diabetes

Diabetes care, 2018-10, Vol.41 (10), p.2178-2186

2018

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Statistical challenges in longitudinal microbiome data analysis

Briefings in bioinformatics, 2022-07, Vol.23 (4)

2022

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Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

Nature methods, 2019-06, Vol.16 (6), p.479-487

2019

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integrOmics: an R package to unravel relationships between two omics datasets

Bioinformatics, 2009-11, Vol.25 (21), p.2855-2856

2009

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PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data

Briefings in bioinformatics, 2023-03, Vol.24 (2)

2023

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Human hepatocellular carcinomas with a periportal phenotype have the lowest potential for early recurrence after curative resection

Hepatology (Baltimore, Md.), 2017-11, Vol.66 (5), p.1502-1518

2017

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Altered Repertoire Diversity and Disease‐Associated Clonal Expansions Revealed by T Cell Receptor Immunosequencing in Ankylosing Spondylitis Patients

Arthritis & rheumatology (Hoboken, N.J.), 2020-08, Vol.72 (8), p.1289-1302

2020

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MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms

BMC bioinformatics, 2017-02, Vol.18 (1), p.128-128, Article 128

2017

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Biomarker development for axial spondyloarthritis

Nature reviews. Rheumatology, 2020-08, Vol.16 (8), p.448-463

2020

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MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities

PloS one, 2016-08, Vol.11 (8), p.e0160169-e0160169

2016

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How does the early life environment influence the oral microbiome and determine oral health outcomes in childhood?

BioEssays, 2021-09, Vol.43 (9), p.e2000314-n/a

2021

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Multivariate Analysis of Multiple Datasets: a Practical Guide for Chemical Ecology

Journal of chemical ecology, 2018-03, Vol.44 (3), p.215-234

2018

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A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

BMC bioinformatics, 2012-12, Vol.13 (1), p.325-325, Article 325

2012

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Variable selection in microbiome compositional data analysis

NAR genomics and bioinformatics, 2020-06, Vol.2 (2)

2020

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Genome-wide characterization of the routes to pluripotency

Nature (London), 2014-12, Vol.516 (7530), p.198-206

2014

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Variable selection for generalized canonical correlation analysis

Biostatistics (Oxford, England), 2014-07, Vol.15 (3), p.569-583

2014

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A Generic Multivariate Framework for the Integration of Microbiome Longitudinal Studies With Other Data Types

Frontiers in genetics, 2019-11, Vol.10, p.963-963

2019

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Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references

Briefings in bioinformatics, 2022-05, Vol.23 (3)

2022

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Dietary intake influences gut microbiota development of healthy Australian children from the age of one to two years

Scientific reports, 2019-08, Vol.9 (1), p.12476-11, Article 12476

2019

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Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets

BMC bioinformatics, 2012-02, Vol.13 (1), p.24-24, Article 24

2012

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Time-course analysis of metabolomic and microbial responses in anaerobic digesters exposed to ammonia

Chemosphere (Oxford), 2021-11, Vol.283, p.131309-131309, Article 131309

2021

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Multivariate Data Integration Using R: Methods and Applications with the mixOmics Package

mixOmics: An R package for 'omics feature selection and multiple data integration

DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems

Intestinal Metaproteomics Reveals Host-Microbiota Interactions in Subjects at Risk for Type 1 Diabetes

Statistical challenges in longitudinal microbiome data analysis

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

integrOmics: an R package to unravel relationships between two omics datasets

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data

Human hepatocellular carcinomas with a periportal phenotype have the lowest potential for early recurrence after curative resection

Altered Repertoire Diversity and Disease‐Associated Clonal Expansions Revealed by T Cell Receptor Immunosequencing in Ankylosing Spondylitis Patients

MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms

Biomarker development for axial spondyloarthritis

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities

How does the early life environment influence the oral microbiome and determine oral health outcomes in childhood?

Multivariate Analysis of Multiple Datasets: a Practical Guide for Chemical Ecology

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

Variable selection in microbiome compositional data analysis

Genome-wide characterization of the routes to pluripotency

Variable selection for generalized canonical correlation analysis

A Generic Multivariate Framework for the Integration of Microbiome Longitudinal Studies With Other Data Types

Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references

Dietary intake influences gut microbiota development of healthy Australian children from the age of one to two years

Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets

Time-course analysis of metabolomic and microbial responses in anaerobic digesters exposed to ammonia

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