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https://www.immport.org/home

Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.

Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy   

•   Source: SciCrunch Registry

http://www.geworkbench.org

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include: * loading data from local or remote data sources. * visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways. * providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory networks reconstruction, BLAST searches, pattern/motif discovery, etc. * validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks (one of the 7 National Centers for Biomedial Computing funded through the NIH Roadmap). Additionally, geWorkbench is supported by caBIG, NCI''s cancer Biomedical Informatics Grid initiative.

Proper citation: genomics Workbench (RRID:SCR_013599) Copy   

•   Source: SciCrunch Registry

http://www.metabolomicsworkbench.org

Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.

Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy   

•   Source: SciCrunch Registry

http://chavi-id.org

A consortium whose goal is to further HIV research and accelerate the development of a preventative HIV vaccine. Its main research target is to define immunogens and immunization regimens that induce sustained HIV cross-protective B cell and CD4+ T cell responses.

Proper citation: CHAVI-ID (RRID:SCR_014047) Copy   

•   Source: SciCrunch Registry

https://nih.figshare.com/

Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com.

Proper citation: NIH Figshare Archive (RRID:SCR_017580) Copy   

•   Source: SciCrunch Registry

https://amoebadb.org/amoeba/

Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers.

Proper citation: AmoebaDB (RRID:SCR_017592) Copy   

•   Source: SciCrunch Registry

https://dandiarchive.org

Free, cloud-based platform for publishing, sharing, and processing standardized neurophysiology data, primarily using the Neurodata Without Borders (NWB) format. Supported by the BRAIN Initiative, it enables researchers to collaborate, reuse datasets, and adhere to FAIR data principles.

Proper citation: Distributed Archives for Neurophysiology Data Integration (RRID:SCR_017571) Copy   

•   Source: SciCrunch Registry

https://bioinformaticshome.com/tools/rna-seq/descriptions/LIGER.html

Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets.

Proper citation: LIGER (RRID:SCR_018100) Copy   

•   Source: SciCrunch Registry

https://github.com/galaxyproteomics/mvpapplication-git.git

Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach.

Proper citation: Multi-omics Visualization Platform (RRID:SCR_018077) Copy   

•   Source: SciCrunch Registry

https://icite.od.nih.gov/covid19/search/

NIH comprehensive, curated source for publications related to COVID-19. Includes articles from PubMed and pre-prints from arXiv, medRxiv, bioRxiv, and ChemRxiv. Updated daily. NIH Office of Portfolio Analysis has developed this resource to explore and analyze set of advances in COVID‑19 research as they accumulate in real time, and complements efforts by NLM to aggregate full text documents broadly related to COVID-19 and other outbreaks, and articles on COVID‑19 specific to PubMed database.

Proper citation: NIH COVID-19 Portfolio (RRID:SCR_018295) Copy   

•   Source: SciCrunch Registry

http://glycam.org/

Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates.

Proper citation: GLYCAM-Web (RRID:SCR_018260) Copy   

•   Source: SciCrunch Registry

https://ncats.nih.gov/n3c/about

Portal for centralized national data to study COVID-19 and identify potential treatments.Centralized, secure analytics platform where patient privacy is protected. Enables collection and analysis of clinical, laboratory and diagnostic data from hospitals and health care plans. Data are provided after executing data transfer agreement with National Center for Advancing Translational Sciences. N3C is partnership among NCATS supported Clinical and Translational Science Awards Program hubs and National Center for Data to Health with overall stewardship by NCATS.

Proper citation: National COVID Cohort Collaborative (RRID:SCR_018757) Copy   

•   Source: SciCrunch Registry

https://bivi.co/visualisation/apinatomy

Software toolkit for visualizing multiscale anatomy schematics with phenotype related information. Used for visualisation of multiscale physiology circuitboards and to support clinical and scientific graphical user interfaces and dashboards for biomedical resource management and data analytics. Creates FAIR models of vascular and neural connectivity information for molecular, subcellular, cellular and tissue conduits across multiple scales. Provides interface between physiology knowledge and data relevant to physiology through intuitive graphical interface for managing semantic metadata and ontologies relevant to physiology. Brings together expertise in computer science, image processing, bioengineering and medicine to manage knowledge in physiology and pathology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ApiNATOMY (RRID:SCR_018998) Copy   

•   Source: SciCrunch Registry

https://portal.imaging.datacommons.cancer.gov

Portal for finding and analyzing cancer imaging data. Part of Cancer Research Data Commons to support cancer imaging research. Provides cloud based access to medical imaging data and library of analytical tools and workflows to share, analyze, and visualize multi modal imaging data from both clinical and basic cancer research studies.

Proper citation: NCI Imaging Data Commons (RRID:SCR_019127) Copy   

•   Source: SciCrunch Registry

https://datacommons.cancer.gov

Cloud based data science infrastructure that provides secure access to cancer research data from NCI programs and key external cancer programs. Serves as coordinated resource for public data sharing of NCI funded programs. Users can explore and use analytical and visualization tools for data analysis. Enables to search and aggregate data across repositories including Cancer Data Service, Clinical Trial Data Commons, Genomic Data Commons, Imaging Data Commons, Integrated Canine Data Commons, Proteomic Data Commons.

Proper citation: Cancer Research Data Commons (RRID:SCR_019128) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/monocle-release/docs/

Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.

Proper citation: Monocle2 (RRID:SCR_016339) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/MAST.html

Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Proper citation: MAST (RRID:SCR_016340) Copy   

•   Source: SciCrunch Registry

http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing.

Proper citation: MAxEntScan (RRID:SCR_016707) Copy   

•   Source: SciCrunch Registry

https://www.niaid.nih.gov/

National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases.

Proper citation: NIAID (RRID:SCR_016598) Copy   

•   Source: SciCrunch Registry

https://niaid.github.io/spice/

Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.

Proper citation: SPICE (RRID:SCR_016603) Copy   

•   Source: SciCrunch Registry