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Transcriptomic and metabolomic data integration software tools | Metabolomics

Metabolomics is a rapidly evolving field that holds promise to provide insights into genotype-phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges is providing tools that link metabolite…
KaPPA-View
Dataset

KaPPA-View

A metabolic pathway database which is able to overlay gene-to-gene and/or…

A metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. This…

MetScape
Desktop

MetScape

Provides a bioinformatics framework for the visualization and interpretation of…

Provides a bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data in the context of human metabolism. MetScape allows users to build and…

InCroMAP
Desktop

InCroMAP Integrated analysis of Cross-platform MicroArray and Pathway data

A tool for the analysis and visualization of high-level microarray data from…

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…

Paintomics
Web

Paintomics

An easy-to-use bioinformatics resource that facilitates the integrated visual…

An easy-to-use bioinformatics resource that facilitates the integrated visual analysis of experiments where transcriptomics and metabolomics data have been measured on different conditions for the…

PathVisio
Desktop

PathVisio

A free open-source pathway analysis and drawing software. PathVisio allows you…

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…

MAGI
Web
Desktop

MAGI Metabolite, Annotation, and Gene Integration

Generates metabolite-gene associations. MAGI finds and scores consensus between…

Generates metabolite-gene associations. MAGI finds and scores consensus between metabolite identifications and gene annotations. It associates input sequences to biochemical reactions by assessing…

PITDB
Dataset

PITDB

Compiles a collection of experimentally observed translated genomic elements…

Compiles a collection of experimentally observed translated genomic elements (TGEs) derived from proteomics informed by transcriptomics (PIT) experiments. PITDB includes a record for each TGE…

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OmicsDI
Dataset

OmicsDI Omics Discovery Index

Permits to access, discover and disseminate omics data sets. OmicsDI is an…

Permits to access, discover and disseminate omics data sets. OmicsDI is an open-source platform that can integrate proteomics, genomics, metabolomics and transcriptomics data sets. This platform…

PM
Dataset

PM PhenoMeter

Detects biologically meaningful patterns within metabolite response profiles.…

Detects biologically meaningful patterns within metabolite response profiles. The PM accepts metabolic phenotypes as queries and searches a database for phenotypes that are statistically…

GutCyc
Dataset

GutCyc

Collects Pathway/Genome Databases from the Human Gut. GutCyc is a compendium of…

Collects Pathway/Genome Databases from the Human Gut. GutCyc is a compendium of over 418 environmental pathway genome databases (ePGDBs) constructed from public shotgun metagenome datasets generated…

MarVis-Pathway
Desktop

MarVis-Pathway Marker Visualization Pathway

Allows the user to identify metabolites by annotation of pathways from…

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…

MassTRIX
Web

MassTRIX

Annotates metabolites in high precision mass spectrometry data. MassTRIX marks…

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,…

MapMan
Desktop
Web

MapMan

A user-driven tool that displays large datasets (e.g. gene expression data from…

A user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes. MapMan was developed for use…

MetMask
Desktop

MetMask metabolite masking tool

Integrates metabolite identifiers from local reference libraries and public…

Integrates metabolite identifiers from local reference libraries and public databases that do not depend on a single common primary identifier. MetMask constructs groups of interconnected identifiers…

IMPaLA
Web

IMPaLA

A web tool for the joint pathway analysis of transcriptomics or proteomics and…

A web tool for the joint pathway analysis of transcriptomics or proteomics and metabolomics data. IMPaLA performs over-representation or enrichment analysis with user-specified lists of metabolites…

integrOmics
Desktop

integrOmics

Performs integrative analyses of two types of 'omics' variables that…

Performs integrative analyses of two types of 'omics' variables that are measured on the same samples. integrOmics includes a regularized version of canonical correlation analysis to…

3Omics
Web

3Omics

Serves for the analysis of human data. 3Omics simplifies the data analysis by…

Serves for the analysis of human data. 3Omics simplifies the data analysis by combining the advantages and operations of several existing systems and packages into a single platform. It accepts…

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Optimas-DW
Dataset

Optimas-DW OPTIMAS Data Warehouse

A comprehensive data collection for maize. Optimas-DW integrates data from…

A comprehensive data collection for maize. Optimas-DW integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. A web interface allows…

VitisNet
Dataset

VitisNet

A model of the molecular networks present in grapevines. VitisNet allows…

A model of the molecular networks present in grapevines. VitisNet allows visualization of the dynamic interactions in the transcriptome, proteome, and metabolome within known molecular networks (for…

ProMeTra
Desktop

ProMeTra

An open source framework that provides visualization methods for multi-omics…

An open source framework that provides visualization methods for multi-omics datasets. The open vector based graphics format SVG is used to facilitate the visualization of the results of complex…

INMEX
Web

INMEX INtegrative Meta-analysis of EXpression data

Assists researchers in conducting two common types of analyses - meta-analysis…

Assists researchers in conducting two common types of analyses - meta-analysis of multiple gene expression datasets ( meta-analysis) or joint analysis of a gene expression dataset and a metabolomic…

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