• mixOmics

  • Referenced in 29 articles [sw09508]
  • technologies, such as omics data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative...
  • HMDB

  • Referenced in 9 articles [sw28995]
  • Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small ... intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education...
  • MetaboAnalyst

  • Referenced in 3 articles [sw28993]
  • MetaboAnalyst - statistical, functional and integrative analysis of metabolomics data. The purpose of MetaboAnalyst ... analyzing data arising from high-throughput metabolomics data. It is designed to address two common ... conditions (biomarker discovery); 2) to use the metabolomic data to predict the conditions under study...
  • anNET

  • Referenced in 2 articles [sw35331]
  • network-embedded thermodynamic analysis of quantitative metabolome data. Results: We have developed in Matlab ... anNET with three published Escherichia coli metabolome data sets. Conclusion: Our user-friendly and generalized ... anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism ... anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering...
  • MSEA

  • Referenced in 2 articles [sw16938]
  • identify biologically meaningful patterns in quantitative metabolomic data. Gene set enrichment analysis (GSEA ... similar tools are currently available for understanding metabolomic data. Here, we introduce a web-based ... MSEA offers three different enrichment analyses for metabolomic studies including overrepresentation analysis (ORA), single sample ... descriptors. For non-mammalian or more specialized metabolomic studies, MSEA allows users to provide their...
  • SIRIUS

  • Referenced in 4 articles [sw14027]
  • among the most widely used technologies in metabolomics. Metabolites participate in almost all cellular processes...
  • INMEX

  • Referenced in 4 articles [sw26782]
  • data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data...
  • integrOmics

  • Referenced in 4 articles [sw28007]
  • omics’ data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple...
  • MMG

  • Referenced in 4 articles [sw29328]
  • cases (such as high-throughput proteomics and metabolomics), only very partial observations are available, resulting...
  • OMG

  • Referenced in 3 articles [sw32082]
  • especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck...
  • COVAIN

  • Referenced in 1 article [sw10556]
  • inverse estimation of the differential jacobian from metabolomics covariance data. Metabolomics emerges ... linking genotypes with the corresponding phenotypes. As metabolomics data are high-dimensional, statistical data analysis ... described by us recently. By integrating the metabolomics covariance matrix and the stoichiometric matrix ... sites in the biochemical network based on metabolomics data. COVAIN was primarily developed for metabolomics...
  • IntLIM

  • Referenced in 1 article [sw28989]
  • IntLIM: Integration using Linear Models of metabolomics and gene expression data. Interpretation of metabolomics data ... eased through integration of metabolomics with other ‘omics’ data. The IntLIM package, which includes ... friendly RShiny web app, aims to integrate metabolomics data with transcriptomic data. Unlike other approaches...
  • Metabox

  • Referenced in 1 article [sw28994]
  • Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration. Similar to genomic ... proteomic platforms, metabolomic data acquisition and analysis is becoming a routine approach for investigating biological ... systems. However, computational approaches for metabolomic data analysis and integration are still maturing. Metabox ... analysis, functional analysis and integrative exploration of metabolomic data within proteomic and transcriptomic contexts. With...
  • MetaboLights

  • Referenced in 1 article [sw16939]
  • open-access general-purpose repository for metabolomics studies and associated meta-data. MetaboLights (http://www.ebi.ac.uk ... first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated ... open-access data providers in molecular biology. Metabolomic profiling is an important tool for research...
  • AStream

  • Referenced in 1 article [sw18849]
  • Astream: an R package for annotating LC/MS metabolomic data. Summary: AStream, an R-statistical software ... extracted from liquid chromatography mass spectrometry (LC/MS) metabolomics data, is described. AStream detects isotopic, fragment ... with a fast, reliable tool for summarizing metabolomic data, notably reducing curation time and increasing...
  • CTS

  • Referenced in 1 article [sw33267]
  • based tool to improve standardization of metabolomic reports. Summary: Metabolomic publications and databases use different ... identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG...
  • Dolphin

  • Referenced in 1 article [sw40762]
  • main challenges in nuclear magnetic resonance (NMR) metabolomics is to obtain valuable metabolic information from ... spectra in metabolomics. Dolphin takes advantage of the 2D J-resolved NMR spectroscopy signal dispersion ... well established approaches in NMR metabolomics. Overall, Dolphin produced more accurate results with the added...
  • SMPDB

  • Referenced in 2 articles [sw29378]
  • support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology...
  • BATMAN

  • Referenced in 2 articles [sw34836]
  • Motivation: NMR spectra are widely used in metabolomics to obtain metabolite profiles in complex biological...
  • RFmarkerDetector

  • Referenced in 1 article [sw26714]
  • package RFmarkerDetector: Multivariate Analysis of Metabolomics Data using Random Forests. A collection of tools ... multivariate analysis of metabolomics data, which includes several preprocessing methods (normalization, scaling) and various exploration...