MetaboAnalyst is an easy-to-use, comprehensive platform for metabolomics data analysis, visualization and interpretation. It currently receives over 3 million data analysis jobs per year. Some major milestones include:

• 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)

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 (expressanalyst.ca) since March, 2022.

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 Projection with Public Data module allows users to visually explore their data with a public reference data.

• 2020 - Nature Protocol on MicrobiomeAnalyst
• 2017 - MicrobiomeAnalyst (v1.0)

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)

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

• 2022 - OmicsNet (v2.0)
• 2018 - OmicsNet (v1.0)

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.

• 2021 - OmicsAnalyst (v1.0)

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 personal computer and can process >2,000,000 reads/min while maintaining high accuracy.

• 2021 - Seq2Fun (v1.0)

ExpressAnalyst is a powerful web-based visual analytics platform for comprehensive gene expression profiling, meta-analysis and systems interpretation. It currently supports transcriptomics data for 18 species as well as ortholog tables from Seq2Fun for species-independent RNAseq analysis. Derived from NetworkAnalyst, ExpressAnalyst is dedicated for gene expression profiling through a series of visual analytics - volcano plots, ridgeline plots, heatmaps, enrichment networks, PCA, and UpSet plots.

• 2022 - ExpressAnalyst (v1.0)

mGWAS-Explorer is a user-friendly web-based platform for network-based integrative analysis and visual exploration of mGWAS data - SNPs, genes, metabolites, and diseases. 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.

• 2022 - mGWAS (v1.0)

FastBMD is a computationally efficient implementation of the National Toxicology Program Approach to genomic Dose-Response Modeling. Key features include a simplified workflow, ability to download results at each step, and interactive exploration of pathway-level BMDs. In addition to model organisms, FastBMD is designed to support non-model organisms by enabling an annotation-free pipeline that includes feature sensitivity-based point-of-departure analysis. The final part of the analysis is designed to allow users to interactively explore BMDs at different levels of organizations.

• 2020 - FastBMD (v1.0)

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 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)