• mixOmics

  • Referenced in 21 articles [sw09508]
  • throughput technologies, such as omics data (e.g. transcriptomics, metabolomics or proteomics data) that require...
  • MetaboAnalyst

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

  • Referenced in 2 articles [sw16938]
  • identify biologically meaningful patterns in quantitative metabolomic data. Gene set enrichment analysis (GSEA ... tools are currently available for understanding metabolomic data. Here, we introduce a web-based server ... MSEA offers three different enrichment analyses for metabolomic studies including overrepresentation analysis (ORA), single sample...
  • COVAIN

  • Referenced in 1 article [sw10556]
  • differential jacobian from metabolomics covariance data. Metabolomics emerges as one of the cornerstones in systems ... genotypes with the corresponding phenotypes. As metabolomics data are high-dimensional, statistical data analysis ... provides a complete workflow including uploading data, data preprocessing, uni- and multivariate statistical analysis, Granger ... biochemical network based on metabolomics data. COVAIN was primarily developed for metabolomics data...
  • 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 ... functional analysis and integrative exploration of metabolomic data within proteomic and transcriptomic contexts. With...
  • AStream

  • Referenced in 1 article [sw18849]
  • package for annotating LC/MS metabolomic data. Summary: AStream, an R-statistical software package ... from liquid chromatography mass spectrometry (LC/MS) metabolomics data, is described. AStream detects isotopic, fragment ... feature pairs that fulfill expected relational patterns. Data reduction by AStream allows compounds ... fast, reliable tool for summarizing metabolomic data, notably reducing curation time and increasing consistency...
  • IntLIM

  • Referenced in 1 article [sw28989]
  • gene expression data. Interpretation of metabolomics data is very challenging. Yet it can be eased ... through integration of metabolomics with other ‘omics’ data. The IntLIM package, which includes a user ... RShiny web app, aims to integrate metabolomics data with transcriptomic data. Unlike other approaches, IntLIM...
  • 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...
  • ChemoSpec

  • Referenced in 1 article [sw15966]
  • available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into...
  • INMEX

  • Referenced in 4 articles [sw26782]
  • enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional...
  • RepExplore

  • Referenced in 1 article [sw30166]
  • technical replicate variance in proteomics and metabolomics data analysis. Summary: High-throughput omics datasets often...
  • PyMS

  • Referenced in 1 article [sw11283]
  • PyMS provides functions for reading the raw data files in ANDI-MS and JCAMP ... parallel processing, thus enabling processing of metabolomic data on multiple CPUs or computing clusters. PyMS...
  • MetaboTools

  • Referenced in 0 articles [sw15375]
  • analysis of genome-scale metabolic models. Metabolomic data sets provide a direct read ... revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model ... workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools ... intra-model analysis of extracellular metabolomic data and a resource offering a broad...
  • MetaboLights

  • Referenced in 1 article [sw16939]
  • general-purpose repository for metabolomics studies and associated meta-data. MetaboLights (http://www.ebi.ac.uk/metabolights) ... open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained ... major open-access data providers in molecular biology. Metabolomic profiling is an important tool ... depends on the availability of public open data across a broad range of experimental methods...
  • integrOmics

  • Referenced in 4 articles [sw28007]
  • availability of many ‘omics’ data, such as transcriptomics, proteomics or metabolomics, the integrative or joint ... challenge as most approaches suffer from high data dimensionality. New methodologies need to be developed...
  • specmine

  • Referenced in 0 articles [sw18913]
  • package specmine: Metabolomics and Spectral Data Analysis and Mining ... Provides a set of methods for metabolomics data analysis, including data loading in different formats...
  • HMDB

  • Referenced in 7 articles [sw28995]
  • intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education ... contain or link three kinds of data: 1) chemical data, 2) clinical data...
  • CorrectOverloadedPeaks

  • Referenced in 0 articles [sw16087]
  • package CorrectOverloadedPeaks. Analyzes and modifies metabolomics raw data (generated using GC-APCI-MS, Gas Chromatography...
  • speaq

  • Referenced in 0 articles [sw17792]
  • quantitative analysis of NMR metabolomic profile data. The core of the processing cascade...
  • GADS

  • Referenced in 1 article [sw06405]
  • mass mixture Often quantitative data coming from proteomics and metabolomics studies have irregular distributions spikes ... tested our method on the real data about vertical cup-to-disc ratio, the important...