A package for metabolomics data analysis


The field of metabolomics, one of the omics technologies that have recently revolutionized biological research, provides multiple challenges for data analysis, that have been addressed by several computational tools. However, none addresses the multiplicity of existing techniques and data analysis tasks. Here, we propose a novel R package that provides a set of functions for metabolomics data analysis, including data loading in different formats, pre-processing, univariate and multivariate data analysis, machine learning and feature selection. The package supports the analysis of data from the main experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment, promoting the rapid development and sharing of data analysis pipelines. Below are 3 case studies with a few pipelines of analysis.

Propolis SC

Paper: An integrated computational platform for metabolomics data analysis

Propolis is a substance produced from the collected buds or exudates of plants (resin) by bees. The resin is masticated, salivary enzymes are added, and the partially digested material is mixed with beewax and used in the hive to seal the walls, strengthen the borders of combs, and embalm dead invaders. Recently, this product has been the subject of studies highlighting its pharmacological properties, such as the antimicrobial ...

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Cachexia

Paper: An integrated computational platform for metabolomics data analysis

Cachexia is a complex metabolic syndrome associated with an underlying illness (such as cancer) and characterized by loss of muscle with or without loss of fat mass. Improved approaches for detecting the onset and evolution of muscle wasting would help to manage wasting syndromes and facilitate early intervention. As metabolites produced from tissue breakdown are likely to be a sensitive indicator of muscle wasting, ...

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Cassava PPD

Paper: An integrated computational platform for metabolomics data analysis

Cassava is widely cultivated in tropical and subtropical regions for its starchy tuberous root, a great source of carbohydrates. It has a variety of applications, like animal feeding, culinary or alcoholic beverages. As it is a tropical root, it undergoes PPD, which is characterized by streaks of blue/black in the root vascular tissue, which with time spread and cause a brown discoloration. PPD begins quickly within 24h postharvest and, because of ...

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Cassava Cultivars

Paper: Carotenoid analysis of cassava genotypes roots (Manihot esculenta Crantz) cultivated in southern Brazil using chemometrics tools

Manihot esculenta roots are considered a staple food for many populations with risk of vitamin A deficiency. In cassava, β-carotene is the majoritarian carotenoid with pro-vitamin A activity. As a strategy to reduce the prevalence of deficiency of this vitamin, cassava genotypes with high pro-vitamin A activity have been identified. The aim of this study was to initiate the metabolomics characterization of a cassava ...

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Propolis SJ

Paper: UV-visible scanning spectrophotometry and chemometrics analysis as tools to build descriptive and classification models for propolis from southern Brazil

Propolis is a chemically complex biomass produced by honeybees (Apis mellifera) from plant resins added of salivary enzymes, beeswax, and pollen. Recent studies classified Brazilian propolis into 12 groups based on physiochemical characteristics and different botanical origins. Since propolis quality depends, among other variables, on the local flora which is strongly influenced by (a)biotic factors over the seasons, to unravel ...

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Cedrela fissilis

Paper: UV-Visible spectrophotometry-based metabolomic analysis of Cedrela fissilis Velozzo (Meliaceae) calluses - A screening tool for culture medium composition and cell metabolic profiles

In plant cell cultures aiming at the production of secondary metabolites of industrial interest, the culture medium composition is a decisive step for obtaining cell growth and high yields of the target compound(s). A rapid and reliable methodology for screening metabolic responses to medium composition is fundamental for the development of this biotechnological field. Following this approach, UV-Vis scanning spectrophotometry ...

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