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IMPaLA / Integrated Molecular Pathway-Level Analysis
Allows combined investigation of gene/protein and metabolite datasets with a comprehensive basis of biochemical pathways. IMPaLA can operate over-representation or Wilcoxon enrichment analysis (WEA). It can recognize pathways that may be disregulated on the transcriptional level, the metabolic level or both. This tool permits the identification of additional pathways with changed activity that would not be highlighted when analysis is applied to any of the functional levels alone.
MBRole / Metabolite Biological Role
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Performs overrepresentation (enrichment) analysis of categorical annotations for a set of compounds of interest. These categorical annotations correspond to biological and chemical information available in a number of public databases and software. Although focused on qualitative annotations, MBRole is general and versatile enough to perform functional enrichment analysis in any metabolomic sample (including additional biological and chemical annotations for human metabolites), and hence complements existing software for the rising field of metabolomics.
ChemRICH / Chemical Similarity Enrichment Analysis
Allows users to realize pathway analysis. ChemRICH is a chemical similarity enrichment analysis software for metabolomics datasets utilizing medical subject headings and Tanimoto substructure chemical similarity coefficients. It can cluster metabolites into non-overlapping chemical groups. This tool is useful for clinical and epidemiological studies using blood or urine specimens. It places such exposome chemicals into metabolites sets to perform exposure enrichment analysis that exceeds classic pathway enrichments.
Metabox
Includes widely used statistical methods to process and identify keys entities of input experiments, offers different integrative analysis methodologies and provides interactive visualization to facilitate biological interpretations. Metabox is a bioinformatics toolbox for deep phenotyping analytics that combines data processing, statistical analysis, functional analysis and integrative exploration of metabolomic data within proteomic and transcriptomic contexts. It supports in-depth analysis of metabolomic data by including four analysis modules: data normalization, statistical analysis, network construction and functional analysis.
BiNChE
An enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.
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