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:

• 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 visual analytics platform for comprehensive transcriptomics data analysis, meta-analysis and systems interpretation. It currently supports transcriptomics data (gene lists, gene expression tables or raw RNAseq data) for 17 species. The public server receives around 20,000 jobs monthly. Some major milestones include:

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

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 multi-omics integration by creating and exploring relationships among genes, proteins, miRNAs, metabolites or transcription factors. OmicsNet has been developed for: 1) systems analysis of a single list of molecules; 2) integrative analysis of multiple lists of different types of molecules; and 3) network visualization in 3D. OmicsNet leverages four types of molecular interactions (PPI, TF-gene, miRNA-gene and metabolite-protein). Users can perform various style customization, functional enrichment analysis, target search, and network topology analyses to gain systems-level insights

• 2018 - OmicsNet (v1.0)

OmicsAnalyst offers a wide range of established data-driven approaches for 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 is written in C++ and can run on a personal computer with a limited number of CPUs and memory. It can process >2,000,000 reads/min while maintaining high accuracy in various test data sets.

• 2021 - Seq2Fun (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)

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: