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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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REDCap Resource Report Resource Website 10000+ mentions |
REDCap (RRID:SCR_003445) | REDCap | software resource, web application | Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. | online survey, survey, database, translational research, informatics, workflow, clinical research, clinical, metadata, biomedical, online form, data capture, management, analysis, data sharing, data collection, data standard, best practice, data collection instrument, electronic data capture |
is listed by: Biositemaps is listed by: SoftCite is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA works with: redcap-completion works with: aux-file-upload |
NIH ; UL1 RR029882 ; UL1 TR000062 ; UL1 RR026314 ; UL1 TR000077 ; UL1 RR024975 ; UL1 TR000445 ; G12 RR003051 ; G12 MD007600 ; UL1 RR024150 ; UL1 TR000135 ; R24 HD042849 ; UL1 RR024989 ; UL1 TR000439 |
PMID:23149159 PMID:18929686 |
Software is available at no cost for REDCap Consortium Partners. If not in the consortium, See the Become a Partner page to find more information about joining our group. | nif-0000-33254 | SCR_003445 | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-02-14 02:05:03 | 20615 | |||||
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TeamTat Resource Report Resource Website 1+ mentions |
TeamTat (RRID:SCR_023439) | software resource, web application | Web based collaborative text annotation tool. Used for managing multi-user, multi-label document annotation. Project managers can specify annotation schema for entities and relations and select annotators and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC (uploaded locally or automatically retrieved from PubMed/PMC), and output format is BioC with inline annotations. Displays figures from full text. | Text annotation, team collaboration, collaborative text annotation, | MSIT ; NIH |
PMID:32383756 | Free, Freely available | https://github.com/ncbi-nlp/TeamTat | SCR_023439 | 2026-02-14 02:04:48 | 3 | ||||||||
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ContainerProfiler Resource Report Resource Website 1+ mentions |
ContainerProfiler (RRID:SCR_023770) | software resource | Software tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Implementation leverages facilities provided by Linux operating system that is integral with Docker containers. | Resource profiling, resource utilization, containerized tasks, resource utilization metrics, | NIH R01GM126019; NIH R01GM126019-02S2; NIH U24HG012674; NIH R03AI159286; NSF OAC-1849970 |
DOI:10.48550/arXiv.2005.11491 | Free, Available for download, Freely available | SCR_023770 | 2026-02-14 02:05:00 | 2 | |||||||||
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METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | data access protocol, software resource, web service | Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository. | Annotate data, genomics study, microbiome, metadata, genomics, data |
is related to: NCBI Sequence Read Archive (SRA) is related to: NCBI |
NIH | Free, Freely available | SCR_018494 | METAdata of GEnomics studies on a web based NOTEbook | 2026-02-14 02:04:40 | 1 | ||||||||
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NCI Imaging Data Commons Resource Report Resource Website 1+ mentions |
NCI Imaging Data Commons (RRID:SCR_019127) | NCI IDC | data repository, storage service resource, portal, data or information resource, service resource, disease-related portal, topical portal | 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. | Imaging Data Commons Data, cloud based data analysis, FAIR data, cancer imaging data, metadata |
uses: DICOM standard is related to: FAIRsharing is related to: Cancer Imaging Archive (TCIA) is related to: Cancer Research Data Commons |
Cancer | NIH | Free, Freely available | r3d100014074 | https://doi.org/10.17616/R31NJNCQ | SCR_019127 | National Cancer Institute Imaging Data Commons | 2026-02-14 02:03:46 | 6 | ||||
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Cancer Research Data Commons Resource Report Resource Website 1+ mentions |
Cancer Research Data Commons (RRID:SCR_019128) | CRDC | data repository, storage service resource, portal, data or information resource, service resource, disease-related portal, topical portal | 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. |
is related to: NCI Imaging Data Commons is related to: FAIRsharing is related to: The Cancer Genome Atlas is related to: Cancer Cell Line Encyclopedia is related to: Genomic Data Commons Data Portal (GDC Data Portal) is related to: Proteomic Data Commons |
Cancer | NIH | Restricted | SCR_019128 | NCI Cancer Research Data Commons, NCI CRDC | 2026-02-14 02:03:46 | 9 | |||||||
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FAIR Data Informatics Laboratory Resource Report Resource Website 1+ mentions |
FAIR Data Informatics Laboratory (RRID:SCR_019235) | FAIR Data Informatics Laboratory, FAIR Data Informatics Lab, FDI Laboratory, FDI Lab, FDIL | laboratory portal, data or information resource, organization portal, portal | UCSD based bioinformatics lab composed of several projects in different biomedical disciplines. Established in 2008 as Neuroscience Information Framework and has since expanded to include broader field of biomedical research. Leader in developing and providing novel informatics infrastructure and tools for making data FAIR: Findable, Accessible, Interoperable and Reusable. FAIR Data informatics laboratory develops SciCrunch.org platform. | FAIR Data, Data Integration, Data Federation, RRID, Ontology, Terminology, Semantic knowledge, Knowledge Graph, Data Curation, Neuroscience Information Framework |
is related to: NIDDK Information Network (dkNET) is related to: SciCrunch Registry is related to: Neuroscience Information Framework has parent organization: University of California at San Diego; California; USA is parent organization of: Open Data Commons for Traumatic Brain Injury |
United States Veterans Association ; NIH |
Free, Freely available | SCR_019235 | 2026-02-14 02:03:47 | 1 | ||||||||
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Agilent Bravo NGS Resource Report Resource Website 1+ mentions |
Agilent Bravo NGS (RRID:SCR_019473) | instrument resource | Workstation is built on Bravo automated liquid handling robot preconfigured for library prep and target enrichment using Next-Generation Sequencing protocols. Workstation modules add microplate handling. Intuitive Agilent VWorks software enables setup of preprogrammed protocols and allows users to create custom protocols., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Agilent, NGS, Instrument Equipment, USEDit, | NIH U24NS120055; NIH GM137200 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_019475, Model_Number_Agilent_Bravo_NGS | SCR_019473 | Agilent Bravo NGS Workstation | 2026-02-14 02:03:55 | 3 | ||||||||
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LocusZoom.org Resource Report Resource Website 10+ mentions |
LocusZoom.org (RRID:SCR_021374) | data access protocol, software resource, web service | Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. | Generate interactive plots, shareable plots, GWAS summary statistics, visualizing statistical genetic data, genetic association study | NHGRI HG009976; NIH BOEH15AMP |
DOI:10.1093/bioinformatics/btab186 | Free, Freely available | SCR_021374 | LocusZoom.js | 2026-02-14 02:04:38 | 32 | ||||||||
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LIGER Resource Report Resource Website 10+ mentions |
LIGER (RRID:SCR_018100) | data analysis software, software resource, data processing software, software application | 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. | Single cell genomic, data integration, dataset, cell identity, integrative analysis, gene regulation, disease state, scRNA seq analysis, shared factor among data set, | has parent organization: Broad Institute | NIH | PMID:31178122 | Free, Available for download, Freely available | https://github.com/MacoskoLab/liger | SCR_018100 | Linked Inference of Genomic Experimental Relationships | 2026-02-14 02:03:31 | 12 | ||||||
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Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | data visualization software, data processing software, data analysis software, software application, software resource | 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. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org https://bio.tools/mvp_a |
SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-02-14 02:03:30 | 1 | |||||
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NIH COVID-19 Portfolio Resource Report Resource Website 10+ mentions |
NIH COVID-19 Portfolio (RRID:SCR_018295) | web service, data or information resource, service resource, data access protocol, software resource | 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. | COVID-19 publication, COVID-19 article, COVID-19 data, COVID-19 full text document, COVID-19 pre-print | COVID-19 | NIH | Free, Freely available | SCR_018295 | iSearch COVID-19 portfolio, COVID-19 Portfolio Tool From the Office of Portfolio Analysis, iSearch COVID-19 Portfolio, COVID-19 Portfolio | 2026-02-14 02:03:36 | 17 | ||||||||
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Data and Computational Resources to Address COVID-19 Resource Report Resource Website |
Data and Computational Resources to Address COVID-19 (RRID:SCR_018274) | disease-related portal, data or information resource, portal, topical portal | COVID-19 open access data and computational resources provided by federal agencies, including NIH, public consortia, and private entities. Continuously updated as more information becomes available. These resources are being shared for scientific and public health interests, and content is responsibility of resource organizers. | COVID-19, COVID-19 data, federal agency data, computational resource, public health information, SARS-CoV-2, NIH |
lists: Nextstrain lists: outbreak.info lists: Research Data Alliance Working Group lists: UC Health clinical data warehouse lists: Vivli lists: Cloud resources for COVID-19 research lists: COVID-19 High Performance Computing Consortium lists: Data-Against-COVID Team lists: NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats lists: NIAID Overview of Coronaviruses lists: Schema.org lists: Virus Pathogen Resource (ViPR) lists: Modeling Infectious Disease Agents Study online portal for COVID-19 lists: LitCovid lists: Broad Terra cloud commons for pathogen surveillance lists: COVID-19 research data on Figshare lists: Dimensions COVID-19 publications, datasets and clinical trials lists: COVID-19 Open Research Dataset lists: Global Initiative on Sharing All Influenza Data |
COVID-19 | NIH | Free, Freely available | SCR_018817 | SCR_018274 | Open Access Data and Computational Resources to Address COVID-19, NIH Open-Access Data and Computational Resources to Address COVID-19 | 2026-02-14 02:03:33 | 0 | ||||||
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GLYCAM-Web Resource Report Resource Website 50+ mentions |
GLYCAM-Web (RRID:SCR_018260) | web service, portal, data or information resource, data access protocol, software resource, topical portal | 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. | Glycosylated SARS-Cov-2 Spike protein, SARS-Cov-2, SARS-Cov-2 Spike protein, spike protein, 3D structure, carbohydrate, oligosaccharide conformation, modeling, structure modeling, data | has parent organization: University of Georgia; Georgia; USA | COVID-19, COVID19 | NIH | Free, Freely available | SCR_018260 | GLYCAM | 2026-02-14 02:03:18 | 96 | |||||||
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National COVID Cohort Collaborative Resource Report Resource Website 100+ mentions |
National COVID Cohort Collaborative (RRID:SCR_018757) | N3C | data repository, storage service resource, portal, data or information resource, service resource, disease-related portal, topical portal | 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. | COVID-19, national data resource, study COVID-19, COVID-19 data, COVID-19 treatment identification, NCATS, clinical data, laboratory data, diagnostic data, health care, analytics platform, patient privacy | COVID-19 | NIH | r3d100013422 | https://doi.org/10.17616/R31NJMUM | SCR_018757 | 2026-02-14 02:03:40 | 115 | |||||||
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ApiNATOMY Resource Report Resource Website 1+ mentions |
ApiNATOMY (RRID:SCR_018998) | data visualization software, data processing software, software toolkit, software application, software resource | 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. | Ontology visualization, physiology circuitboards visualization, biomedical resource management, data analytics, vascular connectivity, neural connectivity, physiology data, metadata, physiology ontology, |
is used by: SPARC Portal has parent organization: University College London; London; United Kingdom has parent organization: University of Auckland; Auckland; New Zealand is organization facet of: SPARC Portal |
NIH OD030541 | PMID:22616108 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018998 | 2026-02-14 02:03:47 | 1 | ||||||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 500+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | ontology, data repository, storage service resource, portal, data or information resource, service resource, controlled vocabulary, disease-related portal, topical portal, database | 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. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | NIH ; NIAID ; DAIT ; NIAID HHSN266200400076C; NIAID HHSN272201200028C |
PMID:24791905 | nlx_152691 | http://www.immport.org/immport-open/public/home/home http://www.immport.org/ |
http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-02-14 02:02:47 | 987 | |||
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DrugCentral Resource Report Resource Website 100+ mentions |
DrugCentral (RRID:SCR_015663) | data or information resource, software resource, database, web application | Database of drug information created and maintained by the Division of Translational Informatics at University of New Mexico. It provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action. | drug, chemical, pharmaceutical, active ingredient, translational informatics, FASEB list | has parent organization: University of New Mexico; New Mexico; USA | NIH 1U54CA189205-01 | PMID:27789690 | Freely Available, Free, Available for download | SCR_015663 | Drug Central, DrugCentral: Online Drug Compendium | 2026-02-14 02:03:04 | 116 | |||||||
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Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | data visualization software, data processing software, software application, software resource, standalone software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rnj, phylogenetic, tree, construction, neighbor, joining, distance, method, reference, standalone, implemetation, relaxed, algorithm, phylogenetic, tree, reconstruction, sequence |
is listed by: Debian is listed by: OMICtools is related to: University of Idaho; Idaho; USA |
NIH P20 RR16448; INBRE Program of the National Center for Research Resources ; NSF EPS 00809035; NIH P20 RR16454 |
PMID:16752216 DOI:10.1007/s00239-005-0176-2 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15083 | https://github.com/ibest/clearcut https://sources.debian.org/src/clearcut/ |
SCR_016059 | 2026-02-14 02:02:58 | 26 | ||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data processing software, data analysis software, software toolkit, software application, software resource | 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. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | NIH DP2 HD088158; Alfred P. Sloan Foundation Research Fellowship |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-02-14 02:03:02 | 203 |
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