maplet: An extensible R toolbox for modular and reproducible omics pipelines

Autor: Chetnik, Kelsey, Benedetti, Elisa, Gomari, Daniel P., Schweickart, Annalise, Batra, Richa, Buyukozkan, Mustafa, Wang, Zeyu, Arnold, Matthias, Zierer, Jonas, Suhre, Karsten, Krumsiek, Jan

This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. It builds on the SummarizedExperiment

Externí odkaz: http://arxiv.org/abs/2105.04305

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Variational autoencoders learn transferrable representations of metabolomics data.

Autor: Gomari, Daniel P.^1,2,3 (AUTHOR), Schweickart, Annalise⁴ (AUTHOR), Cerchietti, Leandro⁵ (AUTHOR), Paietta, Elisabeth⁶ (AUTHOR), Fernandez, Hugo⁷ (AUTHOR), Al-Amin, Hassen⁸ (AUTHOR), Suhre, Karsten⁹ (AUTHOR), Krumsiek, Jan⁴ (AUTHOR) jak2043@med.cornell.edu

Publikováno v: Communications Biology. 6/30/2022, Vol. 5 Issue 1, p1-9. 9p.

A modified Mediterranean‐ketogenic diet favorably modulates the metabolic profiles of mild cognitively impaired individuals.

Autor: Batra, Richa, Huynh, Kevin, Schweickart, Annalise, Neth, Bryan J., Arnold, Matthias, Kastenmuller, Gabi, Meikle, Peter J, Craft, Suzanne, Krumsiek, Jan, Kaddurah‐Daouk, Rima F.

Publikováno v: Alzheimer's & Dementia: The Journal of the Alzheimer's Association; Dec2023 Supplement 15, Vol. 19, p1-2, 2p

A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer's Disease: a serum and CSF-based metabolic analysis.

Autor: Schweickart A; Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA.; Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY 10021, USA., Batra R; Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY 10021, USA., Neth BJ; Department of Neurology, Mayo Clinic, Rochester, MN., Martino C; Department of Pediatrics, University of California San Diego, La Jolla, CA., Shenhav L; Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA., Zhang AR; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA., Shi P; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA., Karu N; Tasmanian Independent Metabolomics and Analytical Chemistry Solutions (TIMACS), Hobart, 7008 Tasmania, Australia., Huynh K; Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, Australia.; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC, Australia., Meikle PJ; Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, Australia.; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC, Australia., Schimmel L; Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA., Dilmore AH; Department of Pediatrics, University of California San Diego, La Jolla, CA., Blennow K; Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden., Zetterberg H; Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden., Blach C; Duke Molecular Physiology Institute, Duke University, Durham, NC, USA., Dorrestein PC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA., Knight R; Departments of Pediatrics, Computer Science and Engineering, Bioengineering, University of California San Diego, La Jolla, CA., Craft S; Department of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston Salem, NC, USA., Kaddurah-Daouk R; Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA.; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA.; Department of Medicine, Duke University, Durham, NC, USA., Krumsiek J; Department of Physiology and Biophysics, Weill Cornell Medicine, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, New York, NY 10021, USA.

Publikováno v: MedRxiv : the preprint server for health sciences [medRxiv] 2023 Nov 27. Date of Electronic Publication: 2023 Nov 27.