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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Duke University Omics Data Analysis Core Facility Resource Report Resource Website |
Duke University Omics Data Analysis Core Facility (RRID:SCR_017174) | service resource, data analysis service, analysis service resource, access service resource, core facility, production service resource, training service resource, data or information resource | Genomic Analysis and Bioinformatics core for data analysis associated with performing complex and data intensive projects in life science research of Duke University and Duke Medical School. Provides expertise, training, data analysis in next generation sequencing, array and proteomic based technologies. | bioinformatics, data, analysis, training, expertise, next, generation, sequencing, array, proteomic, omics | has parent organization: Duke University; North Carolina; USA | Restricted | SCR_017174 | Analysis Core, Resource, Core Facility, Genomic Analysis and Bioinformatics, Duke University, Omics Data | 2026-07-27 09:35:30 | 0 | |||||||||
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Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility Resource Report Resource Website |
Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) | BCF | service resource, data analysis service, database, analysis service resource, access service resource, core facility, production service resource, data or information resource | Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services. | metagenomics, proteomics, protein, structure, functional, genomics, programming, scripting, data | Restricted | SCR_017152 | BCF, Core Facility, University of Oslo, Rikshospitalet-Radiumhospitalet, Bioinformatics | 2026-07-27 09:35:32 | 0 | |||||||||
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Mass spectrometry imaging workbench Resource Report Resource Website 50+ mentions |
Mass spectrometry imaging workbench (RRID:SCR_017410) | software application, software resource, data processing software, data analysis software | Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging. | Analysis, mass, spectrometry, imaging, data, Galaxy, framework, imzML, file, quality, control, visualization, statistics, docker, container | is related to: University of Freiburg; Baden-Wurttemberg; Germany | DOI:10.1101/628719 | Free, Available for download, Freely available | https://github.com/foellmelanie/docker-galaxy-msi, https://galaxyproject.org/use/msi/ | SCR_017410 | 2026-07-27 09:35:39 | 98 | ||||||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | service resource, analysis service resource, software resource, production service resource, portal, data or information resource | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Maryland School of Medicine; Maryland; USA |
NIMH MH114788; NIDCD R01 DC013817; NIMH R24 MH114815; Hearing Health Foundation (Hearing Restoration Project) |
Restricted | SCR_017467 | gene Expression Analysis Resource | 2026-07-27 09:35:33 | 76 | |||||||
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Analysis, Visualization, and Informatics Lab-space (AnVIL) Resource Report Resource Website 10+ mentions |
Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) | AnVIL | service resource, project portal, storage service resource, data repository, portal, data or information resource | Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces. | Dataset, NHGRI, program, NIH, initiative, funded, human, genomic, data, access, sharing, FAIR, analysis, workflow |
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 |
NIH | Restricted | https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL | SCR_017469 | Visualization, and Informatics Lab-space, AnVIL, Analysis Visualization and Informatics Lab-space, Analysis | 2026-07-27 09:35:40 | 24 | ||||||
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Hemodialysis Pilot Studies Consortium Resource Report Resource Website |
Hemodialysis Pilot Studies Consortium (RRID:SCR_017468) | HDPSC | portal, consortium, data or information resource, organization portal | Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium. | Novel, therapy, reduce, morbidity, patient, maintenance, hemodialysis, data, coordinating, center | has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | NIH ; NIDDK |
SCR_017468 | 2026-07-27 09:35:30 | 0 | |||||||||
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Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | software application, software resource, data processing software, data analysis software | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-07-27 09:35:29 | 15 | |||||||||
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miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | database, web service, software resource, data access protocol, data or information resource | Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. | Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Saarland University ; Germany |
PMID:27742822 | biotools:miRPathDb | https://bio.tools/miRPathDB | SCR_017356 | miRNA Pathway Dictionary Database | 2026-07-27 09:35:32 | 52 | ||||||
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fastMNN Resource Report Resource Website 1+ mentions |
fastMNN (RRID:SCR_017351) | software application, software resource, data processing software, data analysis software | Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method. | Correct, batch, effect, single, cell, expression, data, fast, version, mutual, nearest, neighbors | Free, Available for download, Freely available | SCR_017351 | Fast Mutual Nearest Neighbors | 2026-07-27 09:35:38 | 7 | ||||||||||
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Data Information System - DAISY Resource Report Resource Website 1+ mentions |
Data Information System - DAISY (RRID:SCR_017472) | DAISY | web application, software resource | Open source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement. | Map, data, flow, GDPR | Free, Available for download, Freely available | https://github.com/elixir-luxembourg/daisy | SCR_017472 | DAta Information SYstem | 2026-07-27 09:35:30 | 2 | ||||||||
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Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | software application, software resource, data processing software, data analysis software | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
NIBIB EB022911 | Free, Available for downloads, Freely available | SCR_017442 | Mediation Analysis of Causality under Confounding, macc | 2026-07-27 09:35:32 | 0 | |||||||
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redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | service resource, data analysis service, data analysis software, analysis service resource, software resource, software application, production service resource, data processing software | Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data. | microbiome, feature, identify, characterize, analysis, metadata, sample, data | PMID:31239397 | Free, Available for download, Freely available | SCR_017285 | 2026-07-27 09:35:36 | 5 | ||||||||||
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SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | software application, software resource, data acquisition software, data processing software | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | 2026-07-27 09:35:31 | 213 | |||||||||
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SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | ontology, service resource, data analysis service, controlled vocabulary, analysis service resource, production service resource, data or information resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-07-27 09:35:31 | 134 | |||||||
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STRENDA Resource Report Resource Website 1+ mentions |
STRENDA (RRID:SCR_017422) | STRENDA | service resource, database, storage service resource, data repository, data or information resource | Storage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal. | Storage, Beilstein Institut, functional, enzymology, data, complition, validation, dataset, guideline, standard, reporting |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: re3data.org is listed by: FigShare |
Restricted | DOI:10.22011, DOI:10.17616/R3536N, DOI:10.25504/FAIRsharing.ekj9zx, r3d100012329 | http://www.strenda-db.org/, https://doi.org/10.17616/R3536N, https://doi.org/10.17616/r3536n, https://doi.org/10.22011/, https://dx.doi.org/10.22011/, https://fairsharing.org/10.25504/FAIRsharing.ekj9zx, https://doi.org/10.17616/R3536N | SCR_017422 | , Standards for Reporting Enzymology Data, Beilstein-Institut, STRENDA | 2026-07-27 09:35:30 | 3 | ||||||
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SICAS Medical Image Repository Resource Report Resource Website 1+ mentions |
SICAS Medical Image Repository (RRID:SCR_017420) | service resource, storage service resource, data repository | Medical image repository to store medical research data. | Medical, image, repository, store, data |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Free, Freely available | r3d100011560 | https://doi.org/10.17616/R3HP8C | SCR_017420 | Medical Image Repository, SICAS, SICAS Medical Image Repository | 2026-07-27 09:35:39 | 5 | |||||||
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TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | data analysis software, software resource, software application, data processing software, software toolkit | Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019. | temporal, signal, clocklikeness, molecular, phylogeny, visualization, analysis, temporally, sampled, sequenced, data, identify, genetic, incongruent | is related to: BEAST | EU Seventh Framework Programme ; ERC Grant |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | Path-O-Gen, tempest | 2026-07-27 09:35:37 | 152 | ||||||
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European Variation Archive (EVA) Resource Report Resource Website 50+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | service resource, database, storage service resource, data repository, data or information resource | Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser. | Collection, genetic, variation, data, chromosomal, location, dbSNP, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:eva | https://bio.tools/eva | SCR_017425 | EVA, European Variation Archive | 2026-07-27 09:35:30 | 89 | ||||||
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brainGraph Resource Report Resource Website 10+ mentions |
brainGraph (RRID:SCR_017260) | software application, software resource, data processing software, data analysis software | Software R package for performing graph theory analyses of brain MRI data. | graph, theory, analysis, brain, MRI, data |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CRAN |
Free, Available for download, Freely available | https://www.nitrc.org/projects/braingraph/, https://rdrr.io/cran/brainGraph/, https://www.r-pkg.org/pkg/brainGraph | SCR_017260 | brainGraph - Graph Theory Analysis of Brain MRI Data in R, brainGraph | 2026-07-27 09:35:35 | 11 | ||||||||
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Morpheus by Broad Institute Resource Report Resource Website 1000+ mentions |
Morpheus by Broad Institute (RRID:SCR_017386) | service resource, data visualization software, data analysis software, software resource, software application, data processing software | Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis. | Matrix, visualization, analysis, heatmap, input, data, Java | has parent organization: Broad Institute | Free, Available for download, Freely available | https://github.com/cmap/morpheus.js | SCR_017386 | 2026-07-27 09:35:29 | 1704 |
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