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

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Cited by:

  1. Vanessa R. Marcelino & Caitlin Welsh & Christian Diener & Emily L. Gulliver & Emily L. Rutten & Remy B. Young & Edward M. Giles & Sean M. Gibbons & Chris Greening & Samuel C. Forster, 2023. "Disease-specific loss of microbial cross-feeding interactions in the human gut," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  2. Zhaoxiang Cai & Sofia Apolinário & Ana R. Baião & Clare Pacini & Miguel D. Sousa & Susana Vinga & Roger R. Reddel & Phillip J. Robinson & Mathew J. Garnett & Qing Zhong & Emanuel Gonçalves, 2024. "Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  3. Gaoxiang Zhu & Dengfeng Gao & Linzi Li & Yixuan Yao & Yingjie Wang & Minglei Zhi & Jinying Zhang & Xinze Chen & Qianqian Zhu & Jie Gao & Tianzhi Chen & Xiaowei Zhang & Tong Wang & Suying Cao & Aijin M, 2023. "Generation of three-dimensional meat-like tissue from stable pig epiblast stem cells," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  4. Wei Liu & Huaqin He & Davide Chicco, 2024. "Gene signatures for cancer research: A 25-year retrospective and future avenues," PLOS Computational Biology, Public Library of Science, vol. 20(10), pages 1-10, October.
  5. Signe Schmidt Kjølner Hansen & Robert Krautz & Daria Rago & Jesper Havelund & Arnaud Stigliani & Nils J. Færgeman & Audrey Prézelin & Julie Rivière & Anne Couturier-Tarrade & Vyacheslav Akimov & Blago, 2024. "Pulmonary maternal immune activation does not cross the placenta but leads to fetal metabolic adaptation," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
  6. Kristin M. Ham & Layne K. Bower & Shanping Li & Hernan Lorenzi & Safiatou Doumbo & Didier Doumtabe & Kassoum Kayentao & Aissata Ongoiba & Boubacar Traore & Peter D. Crompton & Nathan W. Schmidt, 2024. "The gut microbiome is associated with susceptibility to febrile malaria in Malian children," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  7. Cemal Erdem & Sean M. Gross & Laura M. Heiser & Marc R. Birtwistle, 2023. "MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  8. Zhongheng Zhang & Lin Chen & Hongjie Shen & Jing Wang & Jie Yang & Suibi Yang & Weimin Zhang & Xuandong Jiang & Xiaojun Wu & Xianglin Meng & Fengzhi Zhao & Wanjie Gu & Haiyan Yin & Lihui Wang & Yuetia, 2025. "Deriving consensus sepsis clusters via goal-directed subgroup identification in multi-omics study," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  9. Hannah Voß & Simon Schlumbohm & Philip Barwikowski & Marcus Wurlitzer & Matthias Dottermusch & Philipp Neumann & Hartmut Schlüter & Julia E. Neumann & Christoph Krisp, 2022. "HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  10. Jakub Idkowiak & Jonas Dehairs & Jana Schwarzerová & Dominika Olešová & Jacob X. M. Truong & Aleš Kvasnička & Marios Eftychiou & Ruben Cools & Xander Spotbeen & Robert Jirásko & Vullnet Veseli & Marco, 2025. "Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
  11. Tatjana Sajic & Matej Vizovišek & Stephan Arni & Rodolfo Ciuffa & Martin Mehnert & Sébastien Lenglet & Walter Weder & Hector Gallart-Ayala & Julijana Ivanisevic & Marija Buljan & Aurelien Thomas & Sve, 2025. "Depletion-dependent activity-based protein profiling using SWATH/DIA-MS detects serine hydrolase lipid remodeling in lung adenocarcinoma progression," Nature Communications, Nature, vol. 16(1), pages 1-24, December.
  12. Matthew S. Bramble & Victor Fourcassié & Neerja Vashist & Florence Roux-Dalvai & Yun Zhou & Guy Bumoko & Michel Lupamba Kasendue & D’Andre Spencer & Hilaire Musasa Hanshi-Hatuhu & Vincent Kambale-Mast, 2024. "Glutathione peroxidase 3 is a potential biomarker for konzo," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  13. Tomás Clive Barker-Tejeda & Elisa Zubeldia-Varela & Andrea Macías-Camero & Lola Alonso & Isabel Adoración Martín-Antoniano & María Fernanda Rey-Stolle & Leticia Mera-Berriatua & Raphaëlle Bazire & Pau, 2024. "Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  14. Maria Serena Paladini & Benjamin A. Yang & Kristof A. Torkenczy & Elma S. Frias & Xi Feng & Karen Krukowski & Rene Sit & Maurizio Morri & Wendy Lam & Valentina Pedoia & Stefka Tyanova & Marco Colonna , 2025. "Fate mapping of peripherally-derived macrophages after traumatic brain injury in mice reveals a long-lasting population with a distinct transcriptomic signature," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  15. Mathilde Valenchon & Fabrice Reigner & Gaëlle Lefort & Hans Adriaensen & Amandine Gesbert & Philippe Barrière & Yvan Gaude & Frederic Elleboudt & Isabelle Lévy & Camille Ducluzeau & Joëlle Dupont & An, 2026. "Affiliative behaviours regulate allostasis development and shape biobehavioural trajectories in horses," Nature Communications, Nature, vol. 17(1), pages 1-18, December.
  16. Efrat Muller & Itamar Shiryan & Elhanan Borenstein, 2024. "Multi-omic integration of microbiome data for identifying disease-associated modules," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  17. Dmitry Kobak & Yves Bernaerts & Marissa A. Weis & Federico Scala & Andreas S. Tolias & Philipp Berens, 2021. "Sparse reduced‐rank regression for exploratory visualisation of paired multivariate data," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 70(4), pages 980-1000, August.
  18. David Martino & Nina Kresoje & Nelly Amenyogbe & Rym Ben-Othman & Bing Cai & Mandy Lo & Olubukola Idoko & Oludare A. Odumade & Reza Falsafi & Travis M. Blimkie & Andy An & Casey P. Shannon & Sebastian, 2024. "DNA Methylation signatures underpinning blood neutrophil to lymphocyte ratio during first week of human life," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  19. Zhihao Zhang & Yongqin Liu & Weishu Zhao & Keshao Liu & Yuying Chen & Feng Wang & Guannan Mao & Mukan Ji, 2025. "Distinct genes and microbial communities involved in nitrogen cycling between monsoon- and westerlies-dominated Tibetan glaciers," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  20. Fahad Paryani & Ji-Sun Kwon & Christopher W. Ng & Kelly Jakubiak & Nacoya Madden & Kenneth Ofori & Alice Tang & Hong Lu & Shengnan Xia & Juncheng Li & Aayushi Mahajan & Shawn M. Davidson & Anna O. Bas, 2024. "Multi-omic analysis of Huntington’s disease reveals a compensatory astrocyte state," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
  21. Yechun Hong & Zongjun Yu & Qian Zhou & Chunyu Chen & Yuqiong Hao & Zhen Wang & Jian-Kang Zhu & Hongwei Guo & Ancheng C. Huang, 2024. "NAD+ deficiency primes defense metabolism via 1O2-escalated jasmonate biosynthesis in plants," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  22. Martin, Manon & Govaerts, Bernadette, 2019. "Feature Selection in metabolomics with PLS-derived methods," LIDAM Discussion Papers ISBA 2019020, Université catholique de Louvain, Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA).
  23. Luis V Valcárcel & Edurne San José-Enériz & Xabier Cendoya & Ángel Rubio & Xabier Agirre & Felipe Prósper & Francisco J Planes, 2022. "BOSO: A novel feature selection algorithm for linear regression with high-dimensional data," PLOS Computational Biology, Public Library of Science, vol. 18(5), pages 1-29, May.
  24. Gaowen Yang & Masahiro Ryo & Julien Roy & Daniel R. Lammel & Max-Bernhard Ballhausen & Xin Jing & Xuefeng Zhu & Matthias C. Rillig, 2022. "Multiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
  25. Oto Hanuš & Eva Samková & Jindřich Čítek & Hana Nejeschlebová & Eva Dadáková & Lucie Hasoňová & Michael Rost & Irena Němečková & Karolína Reindl & Markéta Borková & Ondřej Elich, 2024. "The stability of fatty acids in yoghurts produced from bulk milk samples intentionally selected according to dairy production systems," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 69(8), pages 303-316.
  26. Shweta Godbole & Hannah Voß & Antonia Gocke & Simon Schlumbohm & Yannis Schumann & Bojia Peng & Martin Mynarek & Stefan Rutkowski & Matthias Dottermusch & Mario M. Dorostkar & Andrey Korshunov & Thoma, 2024. "Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
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