ArticleGigaScience2018
Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A review of omics approaches to study preeclampsia.Placenta · 2020Pooled it
- Article
- Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.Briefings in bioinformatics · 2024Review
- PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.PLoS computational biology · 2024Article
- PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.bioRxiv : the preprint server for biology · 2024Article
- Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine.Computational and structural biotechnology journal · 2023Review
- Article
- Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses.Metabolites · 2021Review
- Plasma lipid metabolites associate with diabetic polyneuropathy in a cohort with type 2 diabetes.Annals of clinical and translational neurology · 2021Article
- Coupling Machine Learning and Lipidomics as a Tool to Investigate Metabolic Dysfunction-Associated Fatty Liver Disease. A General Overview.Biomolecules · 2021Review
- Lilikoi V2.0: a deep learning-enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data.GigaScience · 2021Article
- Genistein Reduces the Risk of Local Mammary Cancer Recurrence and Ameliorates Alterations in the Gut Microbiota in the Offspring of Obese Dams.Nutrients · 2021Article
- Identifying Significant Metabolic Pathways Using Multi-Block Partial Least-Squares Analysis.Journal of proteome research · 2020Article
- Prepregnant Obesity of Mothers in a Multiethnic Cohort Is Associated with Cord Blood Metabolomic Changes in Offspring.Journal of proteome research · 2020Article
- Metabolomics: A Way Forward for Crop Improvement.Metabolites · 2019Review
- The metaRbolomics Toolbox in Bioconductor and beyond.Metabolites · 2019Review
- Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data.GigaScience · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Lilikoi (the Hawaiian word for passion fruit) is a new and comprehensive R package for personalized pathway-based classification modeling using metabolomics data. Four basic modules are presented as the backbone of the package: feature mapping module, which standardizes the metabolite names provided by users and maps them to pathways; dimension transformation module, which transforms the metabolomic profiles to personalized pathway-based profiles using pathway deregulation scores; feature selection module, which helps to select the significant pathway features related to the disease phenotypes; and classification and prediction module, which offers various machine learning classification algorithms. The package is freely available under the GPLv3 license through the github repository at: https://github.com/lanagarmire/lilikoi and CRAN: https://cran.r-project.org/web/packages/lilikoi/index.html.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.