Metascape is a web-based gene annotation and analysis resource designed to help experimental biologists interpret systems-level and multi-omics datasets. The platform integrates functional enrichment analysis, pathway and process annotation, protein-protein interaction analysis, gene annotation, and membership analysis across numerous biological knowledgebases. Metascape provides streamlined, automated analyses and intuitive visualizations that enable researchers to identify biological pathways, molecular networks, and functional relationships within one or multiple gene lists. It is particularly useful for translating large-scale transcriptomic and other omics datasets into biologically interpretable findings.
CarpeDiem Data Browser is an interactive, open-source visualization platform for exploring patient trajectories and daily ICU clinical data from the SCRIPT CarpeDiem Dataset. Researchers can examine longitudinal clinical features, pneumonia diagnoses, BAL findings, and treatment responses to generate hypotheses and study disease progression in critically ill patients. GitHub: https://github.com/NUSCRIPT/CarpeDiem.
scRNA-seq Data Browser is an interactive portal that enables researchers to explore multi-omic and clinical data from a large cohort of critically ill patients with pneumonia. The platform provides access to single-cell RNA sequencing, multi-omic factor analysis, differential gene expression, and pathway-level analyses that were used to identify pathogen-specific host response patterns and distinct pneumonia endotypes in the human lung as part of Markov et al., 2026.
Outbreak.info is a functional genomic surveillance platform that integrates host- and population-level surveillance data from clinical and wastewater samples with experimental data, including high-throughput deep mutational scanning, to identify emerging mutations and lineages with the potential to adversely impact public health. We have deployed this platform to monitor the spread of highly pathogenic avian influence H5N1 in dairy cattle across the United States (https://h5n1.outbreak.info/) and to track the global spread of SARS-CoV-2 through both clinical (https://outbreak.info/) and wastewater surveillance (https://outbreak.info/wastewater).
Software
OMOP_to_Graph is an open-source framework that converts clinical data stored in the OMOP Common Data Model (CDM) into a graph database structure using Neo4j, facilitating relationship-based analyses of complex clinical datasets.
iVar is a computational package designed for viral amplicon-based sequencing. While its capabilities exist in separate programs, iVar consolidates the specific tools needed to call consensus sequences and intrahost single-nucleotide variants (iSNVs) across multiple replicates. Its key functions include (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling – both iSNVs and insertions/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.
Freya is a tool to estimate relative abundance of SARS-CoV-2 lineages from sequencing of mixed-lineage virus samples, like wastewater. Freyja builds on iVar and is composed of two main steps: (1) SNV frequency estimation and (2) depth-weighted demixing using constrained least absolute deviation regression. Additional post-processing methods are available for output aggregation and visualization.
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies, but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple-to-use user-interface program for setting up standard analyses and a suit of programs for analyzing the results.
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics software. It can make use of multi-core CPUs through multi-threading and fine-grained vectorization using SIMD extensions, and graphics processing units through CUDA and OpenCL. BEAGLE is used by several sophisticated phylogenetics software including BEAST, BEAST2, MyBayes, PhyML, and RevBayes.
AbStar is a software package that is able to perform VDJ assignments and primary annotation of antibody and TCR sequencing data. Scalable from a single sequence to billions of sequences and conforms with AIRR data formatting standards.