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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NIH Human Pluripotent Stem Cell Registry Resource Report Resource Website 1+ mentions |
NIH Human Pluripotent Stem Cell Registry (RRID:SCR_003149) | NIH Human Embryonic Stem Cell Registry | material resource, biomaterial supply resource, cell repository | A listing of human embryonic cell lines that are eligible for use in NIH funded research. Those lines that carry disease-specific mutations are noted as such under the line name. Total Eligible Lines = 200. The purpose of the Registry is to provide investigators with: # a unique NIH Code for each cell line that must be used when applying for NIH funding and # contact information to facilitate investigators' acquisition of stem cells. Before submitting a new grant application and supporting materials for consideration of a human embryonic stem cell line, scientists may wish to see what lines are already under consideration: * Human embryonic stem cell lines submitted to NIH that are being reviewed to determine if they may be used in NIH-supported research, http://grants.nih.gov/stem_cells/registry/pending.htm President George W. Bush required that the name of the registry be changed in his Executive Order #13435, issued on June 20, 2007. As a result of this Executive Order, the former National Institutes of Health Human Embryonic Stem Cell Registry will now be called the National Institutes of Health Human Pluripotent Stem Cell Registry. The registry will now include both human embryonic stem cells that were derived consistent with the President's policy of August 9, 2001 and human pluripotent stem cells derived from non-embryonic sources. | embryonic, cell, human, registry, stem cell, embryonic stem cell, cell line, human embryonic stem cell line, human pluripotent stem cell, adult, fetal, mutation |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Wisconsin International Stem Cell Bank is related to: National Stem Cell Bank is related to: NIF Data Federation is related to: Integrated Cell Lines has parent organization: National Institutes of Health |
NIH ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nif-0000-00565 | SCR_003149 | NIH Human Embryonic Stem Cell Registry, National Institutes of Health Human Pluripotent Stem Cell Registry | 2026-02-16 09:46:01 | 7 | ||||||
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App for searching human and mimivirus homologous proteins Resource Report Resource Website 1+ mentions |
App for searching human and mimivirus homologous proteins (RRID:SCR_022140) | data access protocol, software resource, web service | Web interactive and searchable genome wide comparison tool for browsing human and mimivirus homologous proteins. User friendly Shinny app helps users browse protein sequence homology between humans and mimivirus at genome wide level for querying new homologs and generating new hypotheses. | genome wide comparison tool, browsing human and mimivirus homologous proteins, Shinny app, protein sequence homology | NIH R00 CA225633 | Free, Freely available | SCR_022140 | 2026-02-16 09:50:14 | 1 | ||||||||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | software application, data processing software, software toolkit, image processing software, image analysis software, software resource | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NINDS ; NIGMS RC2 GM092519; Wellcome Trust Strategic Award 095931; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; NIH ; NIMH |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, nif-0000-30467, SCR_018407 | https://imagej.net/ij/ http://rsbweb.nih.gov/ij https://imagej.nih.gov/ij/download.html https://imagej.nih.gov/ij/ https://sources.debian.org/src/imagej/ |
https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-02-16 09:46:06 | 27070 | ||||
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Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) Resource Report Resource Website 50+ mentions |
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) | AMP T2D, T2DKP | data repository, database, storage service resource, topical portal, portal, service resource, data or information resource, disease-related portal | Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease. | type 2 diabetes, diabetes, knowledge, portal, database, repository, type II, diabetic, genetic, data, analysis, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Consortia-pedia is listed by: NIDDK Information Network (dkNET) is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus is related to: Type 1 Diabetes Knowledge Portal is related to: Common Metabolic Diseases Knowledge Portal has parent organization: Foundation for the National Institutes of Health has parent organization: Accelerating Medicines Partnership |
Type 2 diabetes, Diabetes | NIH ; University of Michigan ; Broad Institute ; Fundacion Carlos Slim ; NIDDK |
Free, Freely available | SCR_014533, nlx_157976 | http://www.nih.gov/science/amp/type2diabetes.htm | SCR_003743 | , AMP Diabetes, AMP, T2D, AMP-T2D, Type 2 Diabetes Knowledge Portal, Accelerating Medicines Partnership Type 2 Diabetes, Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal, The AMP-T2D Knowledge Portal, AMP T2D, AMP Type 2 Diabetes | 2026-02-16 09:46:14 | 79 | ||||
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ToRNADo Resource Report Resource Website 50+ mentions |
ToRNADo (RRID:SCR_002706) | software application, data processing software, data visualization software, software resource | A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion. | duplex, protein, rna, visualization | has parent organization: Stanford University; Stanford; California | NIH ; NIGMS R01GM107340; NIGMS U54GM072970 |
Free, Available for download, Freely available | nif-0000-23335 | SCR_002706 | 2026-02-16 09:45:48 | 95 | ||||||||
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Cell Type Ontology Resource Report Resource Website 1+ mentions |
Cell Type Ontology (RRID:SCR_004251) | CL | ontology, data or information resource, controlled vocabulary | Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. | cell ontology, ontology repository |
is listed by: BioPortal is listed by: Ontology Lookup Service is related to: CELDA Ontology is related to: OBO is related to: Cell Line Knowledge Base |
BBSRC ; MRC ; NIH ; NSF DBI-9978564; NSF PGRP-0321666 |
PMID:15693950 | Free, Freely available | nlx_26501 | http://purl.bioontology.org/ontology/CL | http://cellontology.org, http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell, | SCR_004251 | cellontology.org, Obo-cell-type, Cell Ontology | 2026-02-16 09:46:20 | 6 | |||
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CRCNS Resource Report Resource Website 100+ mentions |
CRCNS (RRID:SCR_005608) | CRCNS | funding resource, data repository, collaborative tool, storage service resource, service resource, data or information resource | Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources. | collaborative research, data sharing, computational model, brain, computational neuroscience, data set, FASEB list |
is used by: NIF Data Federation is used by: DataLad is used by: Integrated Datasets is recommended by: National Library of Medicine is listed by: DataCite is related to: Integrated Manually Extracted Annotation has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: University of California; California; USA |
NIH ; NSF IIS-0749049; NSF 0636838 |
PMID:18259695 | Free, Freely available | nif-0000-00255, r3d100011269 | https://api.datacite.org/dois?prefix=10.6080 https://doi.org/10.17616/R31S7P |
SCR_005608 | CRCNS Data sharing, Collaborative Research in Computational Neuroscience - Data sharing, Collaborative Research in Computational Neuroscience, CRCNS - Data sharing | 2026-02-16 09:46:40 | 119 | ||||
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Pubmed Commons Resource Report Resource Website 1+ mentions |
Pubmed Commons (RRID:SCR_014021) | forum, data or information resource, narrative resource, discussion | A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments. | forum, PubMed, commuication |
is listed by: Connected Researchers is related to: PubMed is related to: Connected Researchers |
NIH ; NLM |
Free, Membership required, The community can contribute to this resource | SCR_014021 | 2026-02-16 09:48:27 | 3 | |||||||||
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Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | software application, data processing software, data visualization software, 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 | 2026-02-16 09:48:56 | 26 | ||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | software application, data processing software, software toolkit, data analysis software, 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 | 2026-02-16 09:49:00 | 203 | ||||||||
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MAST Resource Report Resource Website 50+ mentions |
MAST (RRID:SCR_016340) | MAST | software application, data processing software, software toolkit, data analysis software, software resource | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | NIH DP2 DE023321; NIBIB R01 EB008400; Bill and Melinda Gates Foundation OPP1032317 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | Model based Analysis of Single Cell Transcriptomics | 2026-02-16 09:49:00 | 86 | ||||||
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NIAID Resource Report Resource Website 500+ mentions |
NIAID (RRID:SCR_016598) | NIAID | organization portal, topical portal, portal, data or information resource, disease-related portal | National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases. | immunologic, allergic, infectious, disease, institute, treat, prevent |
lists: Nephele lists: PaVE lists: ChemokineDB lists: SPICE lists: TRIAGE lists: NGlycPred lists: dCAS lists: HASP lists: ABC Bacterial Transporter Systems Database lists: TB PORTALS lists: JOINSOLVER is related to: The Immunology Database and Analysis Portal (ImmPort) is related to: The 10000 Immunomes is related to: NIAID Overview of Coronaviruses is parent organization of: OMiCC is parent organization of: OCICB is parent organization of: NetCirChro |
NIH | SCR_016598 | National Institute of Allergy and Infectious Diseases | 2026-02-16 09:49:04 | 510 | ||||||||
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SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | software application, data processing software, data visualization software, data analysis software, software resource | 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. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-02-16 09:49:04 | 66 | ||||
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Cleveland Family Study Resource Report Resource Website 1+ mentions |
Cleveland Family Study (RRID:SCR_016585) | CFS | data or information resource, topical portal, disease-related portal, portal | Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore. | data, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinal | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | NHLBI HL46380; NHLBI T32 HL07567; NIH R01 46380; NCRR M01 RR00080 |
PMID:7881656 | SCR_016585 | Cleveland Family Study | 2026-02-16 09:49:03 | 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 | 2026-02-16 09:50:00 | 32 | ||||||||
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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 | 2026-02-16 09:49:31 | 1 | ||||||||
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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, topical portal, portal, service resource, data or information resource, disease-related 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 | 2026-02-16 09:49:34 | 115 | |||||||
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ApiNATOMY Resource Report Resource Website 1+ mentions |
ApiNATOMY (RRID:SCR_018998) | software application, data processing software, software toolkit, data visualization software, 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 | 2026-02-16 09:49:38 | 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, topical portal, portal, service resource, data or information resource, disease-related 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 | 2026-02-16 09:49:40 | 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, topical portal, portal, service resource, data or information resource, disease-related 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 | 2026-02-16 09:49:36 | 9 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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