Annotates metabolites in high precision mass spectrometry data. MassTRIX marks the identified chemical compounds on KEGG pathway maps using the KEGG/API. Selected genes or enzymes can be highlighted, e.g. to represent information on gene transcription or differences in the gene complement of different bacterial strains.
A free open-source pathway analysis and drawing software. PathVisio allows you to draw, edit and analyse biological pathways. You can visualize your own experimental data on the pathways and find relevant pathways that are over-represented in your data set. PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins. Plugins are available for pathway building, pathway analysis, import/export functionality, data visualization or data integration. Plugins may be developed by anyone by using the PathVisio Plugin API.
Detects the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional correlation nuclear magnetic resonance (NMR) spectrum. ChemSMP is designed to facilitate the analysis of spectra in context of metabolic pathways. It can be categorized into two stages: scoring the chemical shifts of the metabolites on the database side; and comparing the database indexed shifts with the experimentally observed chemical shifts to compute scores for the possible association to metabolic pathways.
Allows the user to identify metabolites by annotation of pathways from cross-omics data. The analysis is supported by an extensive framework for pathway enrichment and meta-analysis. MarVis-Pathway allows the mapping of data set features by ID, name, and accurate mass, and can incorporate information from adduct and isotope correction of mass spectrometry data. It was integrated in the MarVis-Suite, which features the seamless highly interactive filtering, combination, clustering, and visualization of omics data sets.
Assists in collecting, storing, and querying biological pathways. cPath is a scalable, modular, professional-grade software platform. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. It can also provide infrastructure for a large-scale, international effort to pool pathways from multiple sources into common repositories providing convenient integrated points of access for the scientific community.
Offers library searching of data generated from any Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas chromatography-mass spectrometry (GC-MS) platform. AnalyzerPro is a commercial and comprehensive post-processing utility for low and high-resolution LC-MS and GC-MS data with multi-vendor data support. It also provides optimized workflows for sample-to-sample comparison, target component analysis, quantification.
A tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein modification datasets. Several methods are offered that allow for an integrated analysis of data from those platforms. The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signalling pathways.
Allows analysis of mass spectrometry data. MetDAT permits users to combine experiment-centric workflows and data to optimize metabolite analysis. This tool is a web application providing interactive and customizable modules and user-driven analysis of data at hierarchical levels. It standardizes data analysis for researchers and realizes searches to simplify metabolite identification, and pathway mapping. It also contains a rich palette of visualization tools.
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