MetaboAnalyst Users: >500,000

MetaboAnalyst is an easy-to-use, comprehensive platform for metabolomics data analysis, visualization and interpretation. Major milestone releases include:

  • 2024 - MetaboAnalystR (v4.0)
  • 2024 - MetaboAnalyst (v6.0)
  • 2022 - Nature Protocol on MetaboAnalyst
  • 2021 - MetaboAnalyst (v5.0)
  • 2020 - MetaboAnalystR (v3.0)
  • 2019 - MetaboAnalystR (v2.0)
  • 2018 - MetaboAnalystR (v1.0)
  • 2018 - MetaboAnalyst (v4.0)
  • 2015 - MetaboAnalyst (v3.0)
  • 2012 - MetaboAnalyst (v2.0)
  • 2011 - Nature Protocol on MetaboAnalyst
  • 2009 - MetaboAnalyst (v1.0)
MicrobiomeAnalyst Users: >120,000

MicrobiomeAnalyst is an easy-to-use, comprehensive platform for microbiome data analysis. It contains four modules - Marker Data Profiling module offers various options for community profiling, comparative analysis and functional prediction of 16S rRNA data; Shotgun Data Profiling module supports exploratory data analysis, functional profiling and metabolic network visualization of shotgun metagenomics data; Taxon Set Enrichment Analysis module helps interpret taxonomic signatures; and Microbiome Metabolomics Profiling module allows users to perform metabolomics data analysis within the context of the microbiome profiles.

  • 2023 - MicrobiomeAnalyst (v2.0)
  • 2020 - Nature Protocol on MicrobiomeAnalyst
  • 2017 - MicrobiomeAnalyst (v1.0)
ExpressAnalyst Users: ------

ExpressAnalyst is designed as a unified web-based visual analytics platform for comprehensive transcriptomics data analysis. In addition to support >20 species with good reference genomes, ExpressAnalyst leverages our Seq2Fun algorithm and high-resolution ortholog databases (EcoOmicsDB) to enable high-throughput, high-resolution RNAseq analysis in a largely species-independent manner (i.e. RNAseq analysis for species with no or low-quality reference genomes or transcriptomes). ExpressAnalyst is dedicated for gene expression profiling through a series of visual analytics - volcano plots, ridgeline plots, heatmaps, enrichment networks, PCA, and UpSet plots.

  • 2024 - Nature Protocol on Multi-omics
  • 2023 - Current Protocol on ExpressAnalyst
  • 2023 - ExpressAnalyst (v1.0)
OmicsNet Users: >50,000

OmicsNet is a novel network visual analytics system for knowledge-driven multi-omics integration by creating and exploring relationships among SNPs, genes, transcription factors, proteins, miRNAs, metabolites (or LC-MS peaks). OmicsNet leverages four types of molecular interactions (PPI, TF-gene, miRNA-gene and metabolite-protein), two types of annotations (SNP-genes, and peak-metabolite), and one type of prediction (microbe-metabolite). Users can perform various style customization, functional enrichment analysis, target search, and network topology analyses to gain systems-level insights

  • 2024 - Nature Protocol on Multi-omics
  • 2022 - OmicsNet (v2.0)
  • 2018 - OmicsNet (v1.0)
OmicsAnalyst Users: >30,000

OmicsAnalyst offers a wide range of established approaches for data-driven multi-omics integration. It offers three visual analytics tracks: 1) the correlation network analysis track, allowing users to identify important feature and explore their relationships in 2D or 3D networks; 2) the cluster heatmap analysis track, allowing users to apply several cutting-edge multi-view clustering algorithms and explore results using an interactive joint-heatmap; and 3) the dimensionality reduction analysis track, allowing users to apply several multivariate techniques to identify common trends and underlying patterns in interactive 3D scatter plots.

  • 2024 - Nature Protocol on Multi-omics
  • 2021 - OmicsAnalyst (v1.0)
NetworkAnalyst Users: >180,000

NetworkAnalyst is a powerful web-based platform for systems interpretation of gene list data through comprehensive collections of knowledge-based networks - protein-protein interactions, gene regulatory networks, co-expression networks, as well as chemical-, disease- or drug- associated networks. Some major milestones include:

  • 2019 - NetworkAnalyst (v3.0)
  • 2015 - Nature Protocol on NetworkAnalyst (v2.0)
  • 2014 - NetworkAnalyst (v1.0)

Please note its gene expression profiling and meta-analysis modules have been migrated to ExpressAnalyst ( since March, 2022.

miRNet Users: >70,000

miRNet is a comprehensive web application for microRNA functional analysis and systems biology. miRNet offers a wide array of networks connecting miRNAs to genes, metabolites, lncRNAs, epigenetic modifiers, as well as diseases. The system allows users to intuitively explore miRNAs and targets for functional interpretation and hypothesis generation. Since 2018, it also contains a comprehensive list of xeno-miRNAs collected from diverse hosts. The potential target genes of those xeno-miRNAs are also predicted using two popular algorithms.

  • 2020 - miRNet (v2.0)
  • 2016 - miRNet (v1.0)
Seq2Fun Users: ------

Seq2Fun is a all-in-one, ultrafast tool to directly perform functional quantification of RNA-seq reads without transcriptome de novo assembly. It starts with raw read quality control and then conducts a DNA-to-protein search by translating each read into all possible amino acid fragments and subsequently identifies possible homologous sequences in a well-curated protein database. It produces output of read counts annotated with mapped genes for downstream statistical and functional analysis. Seq2Fun can run on a laptop and process >2 million reads/min while maintaining high accuracy. It leverages EcoOmicsDB to enable high-resolution RNAseq analysis in a species-independent manner.

  • 2022 - Seq2Fun (v2.0)
  • 2021 - Seq2Fun (v1.0)
mGWAS-explorer Users: ------

mGWAS-Explorer is a user-friendly web-based platform for causal analysis and interpretation of metabolite-phenotype associations for mGWAS data. Its key features include: 1) comprehensive collection and deep annotation of SNP-metabolite associations based on data from the 65 mGWAS to date; 2) supporting SNP-based, gene-based, metabolite-based network generation to facilitate interpreting results; 3) powerful network visual analytics to gain mechanistic insights as well as for cross-phenotype association analysis. 4) two-sample Mendelian randomization (2S-MR) analysis or causal inference

  • 2023 - mGWAS (v2.0)
  • 2022 - mGWAS (v1.0)
EcoOmicsDB Users: ------

EcoOmicsDB is a companion database for the Seq2Fun algorithm and ExpressAnalyst web platform to provide species-specific evidence for Seq2Fun orthologs. It currently supports over 700 species organized under different taxonomic groups

  • 2023 - EcoOmicsDB (v1.0)
EcoToxXplorer Users: ------

EcoToxXplorer is a web-based platform designed as a data evaluation tool to support quantitative PCR arrays (EcoToxChips). EcoToxChip and EcoToxXplorer work together for the characterization, prioritization, and management of environmental chemicals and complex mixtures of regulatory concern. It currently supports three species including: C. japonica (Japanese quail), C. japonica (fathead minnow), and C. japonica (Africa clawed frog). More species will be added in the near future. For more details, please visit the EcoToxChip Project home page.

  • 2021 - EcoToxXplorer (v1.0)
TrpNet Users: ------

TrpNet is a comprehensive database and analytics platform dedicated to tryptophan metabolism within the context of host (human and mouse) and gut microbiome interactions. TrpNet contains data on tryptophan metabolism involving 130 reactions, 108 metabolites and 91 enzymes across 1246 human gut bacterial species and 88 mouse gut bacterial species. Users can browse, search, and highlight tryptophan metabolic pathway, as well as predict tryptophan metabolites based on a given taxonomy profile using a Bayesian logistic regression model.

  • 2022 - TrpNet (v1.0)
Past Tools

Tools developed in the past have become modules to be maintained and updated together with our current tools. Locations of these tools are given below:

  • FastBMD now part of ExpressAnalyst
  • Xeno-miRNet now part of miRNet
  • INMEX now part of ExpressAnalyst
  • INVEX now part of ExpressAnalyst
  • ROCCET now part of MetaboAnalyst
  • MetPA now part of MetaboAnalyst
  • MSEA now part of MetaboAnalyst
  • MetATT now part of MetaboAnalyst
  • MetaboMiner standalone tool (download)