mixOmics package
- Rohart F., Gautier, B, Singh, A and Lê Cao, K. A. (2017) mixOmics: an R package for ‘omics feature selection and multiple data integration. PLoS Comput Biol 13(11): e1005752.
mixOmics methods
- Singh A, Gautier B, Shannon C, Vacher M, Rohart F, Tebbutt S, K-A. Lê Cao (2019). DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays. Bioinformatics 35(17)
- Rohart F., Matigian N., Eslami A., Bougeard S and Lê Cao, K-A (2017). MINT: A multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms BMC Bioinformatics 18:128.
- K-A. Lê Cao*, ME Costello*, VA Lakis, F Bartolo, XY Chua, R Brazeilles, P Rondeau. (2016) MixMC: Multivariate insights into Microbial Communities. PLoS ONE 11(8): e0160169.
- Tenenhaus A., Phillipe C., Guillemot V., Lê Cao K-A. , Grill J. , Frouin V. (2014),[sgcca] ‘Variable selection for generalized canonical correlation analysis’, Biostatistics, doi: 10.1093/biostatistics. PMID: 24550197.
- González I., Lê Cao K.-A., Davis, M.D. and Déjean S. (2013) [networks and CIM]Insightful graphical outputs to explore relationships between two ‘omics’ data sets. BioData Mining 5:19.
- Yao F., Coquery J., Lê Cao K.-A. (2012) [IPCA] Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets, BMC Bioinformatics 13:24.
- Liquet B, Lê Cao K-A, Hocini H, Thiebaut R (2012). [multilevel] A novel approach for biomarker selection and the integration of repeated measures experiments from two assays. BMC Bioinformatics 13:325.
- Lê Cao K.-A., Boitard S. and Besse P. (2011) [sPLS-DA] Sparse PLS Discriminant Analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinformatics, 22:253.
- González I., Déjean S., Martin P.G.P., Gonçalves O., Besse P. and Baccini A. (2009) [rcc] Highlighting Relationships Between Heteregeneous Biological Data Through Graphical Displays Based On Regularized Canonical Correlation Analysis. Journal of Biological Systems 17(2), pp 173-199.
- Lê Cao K.-A., Martin P.G.P, Robert-Granié C. and Besse, P. (2009) [sPLS] Sparse Canonical Methods for Biological Data Integration: application to a cross-platform study. BMC Bioinformatics, 10:34.
- Lê Cao K.-A., Rossouw D., Robert-Granié C. and Besse P. (2008) [sPLS] A Sparse PLS for Variable Selection when Integrating Omics data. Statistical Applications in Genetics and Molecular Biology 7(1), Article 35.
- González I., Déjean S., Martin P. and Baccini A. (2008) [rcc] CCA: An R package to extend canonical correlation analysis. Journal of Statistical Sofware, 23(12).
mixOmics related methods
These methods are not in the package, but call mixOmics methods and are developed by our team
- Kodikara S, Lê Cao, K. A. (2025) [LUPINE] Microbial network inference for longitudinal microbiome studies with LUPINE, bioRxiv 2024.05.08.593086. Accepted in Microbiome 20/01/2025
- Mao J, Deng Y, Lê Cao, K. A.. Φ-Space: Continuous phenotyping of single-cell multi-omics data. bioRxiv 2024.06.19.599787
- Bodein A, Chapleur O, Droit A and Lê Cao, K. A. (2019) [timeOmics] A generic multivariate framework for the integration of microbiome longitudinal studies with other data types. Frontiers in Genetics
- Bodein A, Scott-Boyer MP, Perin O, Lê Cao, K. A., Droit A (2022) [timeOmics] timeOmics: an R package for longitudinal multi-omics data integration. Bioinformatics 38 (2), 577-579
- Mariette J, Villa-Vialaneix N (2018) [mixKernel] Unsupervised multiple kernel learning for heterogeneous data integration, Bioinformatics, 34(6)
Some publications using mixOmics (with our team)
- DR Bond, SM Burnard, K Uddipto, KV Hunt, BM Harvey, … KA Lê Cao and H Lee. [ MINT, multiblock] Upregulated cholesterol biosynthesis facilitates the survival of methylation-retaining AML cells following decitabine treatment. bioRxiv, 2024.01. 30.577864
- G Kong, S Ellul, VK Narayana, K Kanojia, HTT Ha, S Li, T Renoir, KA Lê Cao, A J Hannan (2021) [mixMC, DIABLO] An integrated metagenomics and metabolomics approach implicates the microbiota-gut-brain axis in the pathogenesis of Huntington’s disease. Neurobiology of Disease 148, 105199
- M Terzin, SJ Robbins, SC Bell, KA Lê Cao, RK Gruber, PR Frade, N S. Webster, YK Yeoh, DG. Bourne & PW. Laffy (2025) [MINT, sPLS] Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef . Microbiome 13 (1), 11
- S Poirier, S Déjean, C Midoux, KA Lê Cao, O Chapleur (2020) [MINT] Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol. Bioresource Technology 316, 123952
- AH Lee, CP Shannon, N Amenyogbe, TB Bennike, J Diray-Arce, OT Idoko, KA Lê Cao, … (2019) [DIABLO] Dynamic molecular changes during the first week of human life follow a robust developmental trajectory. Nature communications 10 (1), 1092
- Maxime H, Nicole F, Lê Cao K-A. (2018) Multivariate analysis of multiple datasets: a practical guide for chemical ecology. Journal of Chemical Ecology, 44(3): 215-234.
- Günther P., Shin H., Ng R.T., McMaster W. R. , McManus B. M. , Keown P. A. , Tebbutt S. J. , Lê Cao K-A. (2014). [sPLS-DA] Novel multivariate methods for integration of genomics and proteomics data: Applications in a kidney transplant rejection study, OMICS: A journal of integrative biology.
- Combes S., González I., Déjean S., Baccini A., Jehl N., Juin H., Cauquil L., Gabinaud B., Lebas F. and Larzul C. (2008) [rcc] Relationships between sensorial and physicochemical measurements in meat of rabbit from three different breeding systems using canonical correlation analysis. Meat Science 3, pp 835-841.
Publications using mixOmics (from independent groups)
The mixOmics package and the mixOmics methods have been cited in thousands of studies. We list below a very few as examples.
- CH Liu, YLLai, PC Shen, HC Liu, et al. (2024) [DIABLO] DriverDBv4: a multi-omics integration database for cancer driver gene research, Nucleic Acids Research, 52(D1)
- M Mazorra-Alonso, JM Peralta-Sánchez, P Heeb et al. (2024) [ PCA, sPLS-DA] Microbiota and the volatile profile of avian nests are associated with each other and with the intensity of parasitism, FEMS Microbiology Ecology, 100 (10)
- M Urrutia, V Meco, JL Rambla, et al. (2023). [sPLS-DA] Diversity of the volatilome and the fruit size and shape in European woodland strawberry (Fragaria vesca). The Plant Journal
- RR Bhatt, S Todorov, R Sood, S Ravichandran, LA Kilpatrick, et al. (2023). [sPLS, DIABLO] Integrated multi-modal brain signatures predict sex-specific obesity status, Brain Communications, 5(2)
- Huang, R., Chen, J., Zhou, M. et al. (2023) [sPLS-DA, PLS-DA, DIABLO] Multi-omics profiling reveals rhythmic liver function shaped by meal timing. Nat Commun 14, 6086.
- Schoeler, M., Ellero-Simatos, S., Birkner, T. et al. (2023) [PCA, sPLS, rCCA, DIABLO] The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis. Nat Commun 14, 5329.
- A Romdhane, A Spor, J Aubert, D Bru, MC Breuil et al. (2022) [DIABLO] Unraveling negative biotic interactions determining soil microbial community assembly and functioning, The ISME Journal, 16 (1)
- Yang, G., Ryo, M., Roy, J. et al. (2022) [DIABLO] Multiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms. Nat Commun 13, 4260.
- Bowerman, K.L., Rehman, S.F., Vaughan, A. et al. (2020) [PCA, sPLS-DA, DIABLO] Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nat Commun 11, 5886 .
- Fettweis, J.M., Serrano, M.G., Brooks, J.P. et al. (2019) [sgcca] The vaginal microbiome and preterm birth. Nat Med 25, 1012–1021.
- Stokholm, J., Blaser, M.J., Thorsen, J. et al. (2018) [sPLS] Maturation of the gut microbiome and risk of asthma in childhood. Nat Commun 9, 141 .
Patents
mixOmics has been used in more than 100 patents , see the Google Patent page.