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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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Strelka2 Resource Report Resource Website 100+ mentions |
Strelka2 (RRID:SCR_005109) | software resource, source code | Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller. | single nucleotide variant, indel, somatic snv, next-generation sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Illumina |
Cancer, Tumor, Normal | PMID:22581179 PMID:30013048 |
Free, Available for download, Freely available | biotools:strelka | https://bio.tools/strelka, https://sources.debian.org/src/strelka/ | http://bioinformatics.oxfordjournals.org/content/early/2012/05/10/bioinformatics.bts271.full.pdf | SCR_005109 | SciCrunch Registry | Strelka | 2026-09-26 02:19:48 | 283 | ||||
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University of Ottawa; Ontario; Canada Resource Report Resource Website 1+ mentions |
University of Ottawa; Ontario; Canada (RRID:SCR_006319) | uOttawa | university | University of Ottawa often referred to as uOttawa or U of O, is a bilingual public research university in Ottawa, Ontario, Canada. |
is parent organization of: Ottawa Hospital Research Institute Labs and Facilities is parent organization of: XplorMed is parent organization of: Peer Review Radio is parent organization of: Subviral RNA Database is parent organization of: StemBase is parent organization of: Ottawa Hospital Research Institute StemCore Laboratories Core Facility is parent organization of: DAMBE is parent organization of: Autonomous Training of a Forelimb Motor Task project is parent organization of: University of Ottawa Louise Pelletier Histology Core Facility is parent organization of: University of Ottawa Preclinical Imaging Core Facility is parent organization of: University of Ottawa Cell Biology and Image Acquisition Core Facility is parent organization of: University of Ottawa Bioinformatics Core Facility is parent organization of: University of Ottawa Genome Editing and Molecular Biology Core Facility is parent organization of: University of Ottawa Flow Cytometry and Virometry Core Facility is parent organization of: Ottawa Hospital Research Institute Flow Cytometry and Cell Sorting Core Facility is parent organization of: University of Ottawa Electron Microscopy Core Facility is parent organization of: Cardio-Neuro-Mind Data Platform is parent organization of: Ottawa Hospital Research Institute Human Pluripotent Stem Cell Core Facility is parent organization of: University of Ottawa Integrated Neurocognitive and Social Psychophysiology Interdisciplinary Research Environment (INSPIRE) Core Facility |
Wikidata Q627969, Crossref Funder ID 100008572, ISNI 0000 0001 2182 2255, GRID grid.28046.38 | https://ror.org/03c4mmv16 | SCR_006319 | SciCrunch Registry | , uOttawa, U of O, University of Ottawa | 2026-09-26 02:19:48 | 4 | ||||||||
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University of Santiago de Compostela; Santiago de Compostela; Spain Resource Report Resource Website |
University of Santiago de Compostela; Santiago de Compostela; Spain (RRID:SCR_007888) | USC | institution, university | is related to: Open PHACTS | SCR_007888 | SciCrunch Registry | Universidade de Santiago de Compostela, University of Santiago de Compostela | 2026-09-26 02:19:50 | 0 | |||||||||||
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Registry Builder Data Harmonization and Aggregation Tool Resource Report Resource Website |
Registry Builder Data Harmonization and Aggregation Tool (RRID:SCR_006559) | Registry Builder Data Harmonization and Aggregation Tool | commercial organization, software resource | Software to harmonize the data that you have in different Excel files, databases, repositories, biospecimen applications, etc. and maps it to one common registry. Remedy Informatics' platform aggregates data from multiple sources, harmonizes the data via Ontology, and provides data visualization and pattern recognition and querying tools. | registry, ontology, visualization, pattern recognition, querying tool | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Mosaic License, Http://www.nitrc.org/include/glossary.php#694 | nlx_155942 | http://www.nitrc.org/projects/registrybuilder | SCR_006559 | SciCrunch Registry | 2026-09-26 02:19:49 | 0 | |||||||
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National Resource for Network Biology Resource Report Resource Website 1+ mentions |
National Resource for Network Biology (RRID:SCR_004259) | NRNB | biomedical technology research center, training resource | Biomedical technology research center that develops new algorithms, visualizations and conceptual frameworks to study biological networks at multiple levels and scales, from protein-protein and genetic interactions to cell-cell communication and vast social networks. They are developing freely available, open-source suite of software technology that broadly enables network-based visualization, analysis, and biomedical discovery for NIH-funded researchers. This software is enabling researchers to assemble large-scale biological data into models of networks and pathways and to use these networks to better understand how biological systems operate under normal conditions and how they fail in disease. The National Resource for Network Biology is organized around the following key components: Technology Research and Development, Driving Biomedical Projects, Outreach, Training and Dissemination of Tools. The NRNB supports several types of training events, including both virtual and live workshops; tutorials sessions for clinicians, biologists and bioinformaticians; presentations and demonstrations at conferences; online tutorials and webcasts; and annual symposium. | protein-protein interaction, interaction, cell, cell communication, network, model, pathway, biological system, disease, visualization, analysis, biomedical, computing and informatics technology center | has parent organization: University of California at San Diego; California; USA | NIGMS GM103504; NCRR RR031228 |
nlx_27231 | SCR_004259 | SciCrunch Registry | 2026-09-26 02:19:47 | 6 | ||||||||
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DNA Chromatogram Explorer Resource Report Resource Website 1+ mentions |
DNA Chromatogram Explorer (RRID:SCR_005585) | Chromatogram Explorer | commercial organization, software resource | A Windows Explorer clone dedicated to DNA sequence analysis and manipulation. View, edit, and convert chromatograms. Trim low quality ends automatically. The Lite version of Chromatogram Explorer is freeware. | chromatogram | is listed by: OMICtools | Commercial license, Free, (Lite version) | OMICS_01018 | SCR_005585 | SciCrunch Registry | DNA Chromatogram Explorer Lite, Chromatogram Explorer Lite | 2026-09-26 02:19:48 | 1 | |||||||
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University of Pittsburgh School of Medicine; Pennsylvania; USA Resource Report Resource Website 1+ mentions |
University of Pittsburgh School of Medicine; Pennsylvania; USA (RRID:SCR_006674) | UPSOM | institution, university |
has parent organization: University of Pittsburgh; Pennsylvania; USA is parent organization of: caTIES - Cancer Text Information Extraction System is parent organization of: National Center for Multiscale Modeling of Biological Systems is parent organization of: EDDA Study Design Terminology is parent organization of: University of Pittsburgh Department of Ophthalmology Tissue Culture and Histology Module Core Facility |
SCR_006674 | SciCrunch Registry | University of Pittsburgh School of Medicine | 2026-09-26 02:19:49 | 2 | |||||||||||
|
Fungal Genome Initiative Resource Report Resource Website 10+ mentions |
Fungal Genome Initiative (RRID:SCR_003169) | FGI | data or information resource, data set | Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics. | sequence, fungi, gene annotation, genome |
is listed by: 3DVC has parent organization: Broad Institute |
NHGRI ; NSF ; NIAID ; USDA |
Free, Freely available | nif-0000-30591 | SCR_003169 | SciCrunch Registry | 2026-09-26 02:19:46 | 18 | |||||||
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University of Ljubljana; Ljubljana; Slovenia Resource Report Resource Website |
University of Ljubljana; Ljubljana; Slovenia (RRID:SCR_004498) | institution, university |
is parent organization of: GenePath is parent organization of: BITOLA: Biomedical Discovery Support System is parent organization of: 1KA |
SCR_004498 | SciCrunch Registry | 2026-09-26 02:19:47 | 0 | |||||||||||||
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XP-CLR Resource Report Resource Website 50+ mentions |
XP-CLR (RRID:SCR_004961) | software resource, source code | XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation are available. | has parent organization: Harvard Medical School; Massachusetts; USA | Restricted | nlx_94751 | https://reich.hms.harvard.edu/software | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004961 | SciCrunch Registry | XP-CLR Software | 2026-09-26 02:19:48 | 74 | |||||||
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D2R Server - Publishing Relational Databases on the Semantic Web Resource Report Resource Website |
D2R Server - Publishing Relational Databases on the Semantic Web (RRID:SCR_004963) | D2R Server | software resource, source code | D2R Server is a tool for publishing relational databases on the Semantic Web. It enables RDF and HTML browsers to navigate the content of the database, and allows applications to query the database using the SPARQL query language. Data on the Semantic Web is modeled and represented in RDF. D2R Server uses a customizable D2RQ mapping to map database content into this format, and allows the RDF data to be browsed and searched the two main access paradigms to the Semantic Web. D2R Server''s Linked Data interface makes RDF descriptions of individual resources available over the HTTP protocol. An RDF description can be retrieved simply by accessing the resource''s URI over the Web. Using a Semantic Web browser like Tabulator (slides) or Disco, you can follow links from one resource to the next, surfing the Web of Data. The SPARQL interface enables applications to search and query the database using the SPARQL query language over the SPARQL protocol. Requests from the Web are rewritten into SQL queries via the mapping. This on-the-fly translation allows publishing of RDF from large live databases and eliminates the need for replicating the data into a dedicated RDF triple store. The latest source code is available from the project''s CVS repository and can be browsed online. | has parent organization: Free University of Berlin; Berlin; Germany | nlx_92812 | SCR_004963 | SciCrunch Registry | 2026-09-26 02:19:48 | 0 | ||||||||||
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Piedmont Health Survey of the Elderly Resource Report Resource Website |
Piedmont Health Survey of the Elderly (RRID:SCR_006349) | PHSE | data or information resource, data set | Data set of a follow-up study (one of four Established Populations for Epidemiologic Studies of the Elderly - EPESE) that obtains information on four primary outcome variables (cognitive status, depression, functional status, and mortality) and four primary independent variables (social support, social class, social location, and chronic illness); and examines the relationships between social factors and chronic disease on the one hand and health outcomes on the other. This data set complements the other three sites providing a population which is both urban and rural and contains approximately equal numbers of black and white participants across a broad socioeconomic base. The Duke site was originally funded by the NIA Epidemiology, Demography and Biometry Program (EDBP) to complete seven waves of data collection (three in-person and four telephone interviews) in order to examine the health of a sample of 4,162 persons aged 65+, and factors that influence their health and use of health services. The cohort was originally interviewed in 1986/87 and followed annually for 6 years thereafter. The study design consisted of a random stratified household sample with an over-sampling of blacks. Questionnaire topics include the following: Demographics, Alcohol Use, Independence, Health condition, Cognition, Personal mastery, Health Service Utilization, Activity of daily living, Social Support, Hearing and Vision, Incontinence, Social Interaction, Weight and Height, Smoking, Religion, Nutrition, Life Satisfaction, Self Esteem, Sleep, Medications, Economic Status, Depression, Life Changes, Blood pressure. National Death Index files have been searched and death certificates obtained for the members of this study. Sample members have been matched with Medicare Part A files to obtain information on hospitalizations, and will be matched on Medicare Part B (outpatient) files. Data from the first wave of the survey is in the public domain and can be obtained from NACDA or from the National Archives, Center for Electronic Records in Washington, DC. * Dates of Study: 1996-1997 * Study Features: Longitudinal, Oversampling * Sample Size: 1986-1988: 4,162 Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02744 * National Archives: http://www.archives.gov/research/electronic-records/ | late adult human, african-american, caucasian, interview, questionnaire, health, health service utilization, cognitive status, functional status, mortality, social support, social class, social location, chronic illness, social factor, chronic disease, health outcome, questionnaire, demographics, alcohol use, independence, health condition, cognition, personal mastery, activity of daily living, social support, hearing, vision, incontinence, social interaction, weight, height, smoking, religion, nutrition, life satisfaction, self esteem, sleep, medication, economic status, depression, life change, blood pressure, survey, chronic illness, disease, epidemiology, hospitalization, long term care, mortality rate, risk factor, death, clinical |
is listed by: Inter-university Consortium for Political and Social Research (ICPSR) is related to: Established Populations for Epidemiologic Studies of the Elderly has parent organization: Duke University School of Medicine; North Carolina; USA has parent organization: National Archive of Computerized Data on Aging (NACDA) |
Aging, All noninstitutionalized persons 65 years of age and older (at baseline, 1986-1987) in Durham, Warren, Vance, Granville, And Franklin counties in north central North Carolina | NIA 1-R01 AG12765 | Public: This product is distributed as a CD-ROM. | nlx_152068 | SCR_006349 | SciCrunch Registry | Piedmont Health Survey of the Elderly (PHSE) Ten-Year Follow-up of the North Carolina EPESE | 2026-09-26 02:19:49 | 0 | |||||
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University of Leipzig; Saxony; Germany Resource Report Resource Website |
University of Leipzig; Saxony; Germany (RRID:SCR_004960) | institution, university |
is affiliated with: Big Data Public Private Forum is related to: PharmaCog is related to: EMIF is parent organization of: OnEx - Ontology Evolution Explorer is parent organization of: RDFaCE is parent organization of: RNAplex is parent organization of: DBpedia is parent organization of: Segemehl is parent organization of: Transfer RNA database is parent organization of: AffyRNADegradation is parent organization of: virtualArray |
SCR_004960 | SciCrunch Registry | Universität Leipzig, University of Leipzig, Universitat Leipzig | 2026-09-26 02:19:48 | 0 | ||||||||||||
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Models of SHM Targeting and Substitution Resource Report Resource Website 1+ mentions |
Models of SHM Targeting and Substitution (RRID:SCR_005250) | S5F | data or information resource, data set | A targeting model that defines where mutations occur (by specifying the relative rates at which DNA motifs in the Ig sequence are mutated), and a nucleotide substitution model that defines the resulting mutation (by specifying the probability of each base mutating to each of the other three possibilities as a function of the surrounding bases). | somatic hypermutation, substitution, targeting, aid, b cell, affinity maturation, immunoglobulin, mutability, mutation, model, targeting model, nucleotide substitution model |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:24298272 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported | OMICS_00302 | SCR_005250 | SciCrunch Registry | S5F - Models of SHM Targeting and Substitution, Models of SHM Targeting and Substitution | 2026-09-26 02:19:48 | 2 | ||||||
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University of Siena; Tuscany; Italy Resource Report Resource Website |
University of Siena; Tuscany; Italy (RRID:SCR_008080) | UNISI | institution, university | is parent organization of: Italian Rett Syndrome database | SCR_008080 | SciCrunch Registry | UNISI | 2026-09-26 02:19:50 | 0 | |||||||||||
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University of Manitoba; Manitoba; Canada Resource Report Resource Website 1+ mentions |
University of Manitoba; Manitoba; Canada (RRID:SCR_003867) | institution, university |
is parent organization of: Manitoba Breast Tumor Bank is parent organization of: University of Manitoba Genomic Centre for Cancer Research and Diagnosis Core Facility is parent organization of: University of Manitoba Grex High Performance Computing Core Facility |
SCR_003867 | SciCrunch Registry | 2026-09-26 02:19:47 | 7 | |||||||||||||
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Beijing: Short TR Study Resource Report Resource Website 1+ mentions |
Beijing: Short TR Study (RRID:SCR_003502) | Beijing Short TR | data or information resource, data set | Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information | nifti, fmri, resting-state fmri, image collection, early adult human, mprage, diffusion tensor imaging, neuroimaging, brain, demographic |
has parent organization: Beijing Normal University; Beijing; China has parent organization: 1000 Functional Connectomes Project |
Healthy | National Natural Science Foundation of China 30770594; National High Technology Program of China 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_157642 | SCR_003502 | SciCrunch Registry | Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Short TR Sample, BNU Short TR Sample | 2026-09-26 02:19:46 | 6 | |||||
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MF-GE Resource Report Resource Website |
MF-GE (RRID:SCR_003509) | MF-GE | software resource, source code | A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map. | microarray, classification, gene |
is listed by: OMICtools has parent organization: University of Sydney; Sydney; Australia |
PMID:20122224 | OMICS_02295 | SCR_003509 | SciCrunch Registry | Multiple Filters enhanced Genetic Ensemble System (MF-GE), Multiple Filters enhanced Genetic Ensemble System | 2026-09-26 02:19:46 | 0 | |||||||
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Medical University of Vienna; Vienna; Austria Resource Report Resource Website |
Medical University of Vienna; Vienna; Austria (RRID:SCR_005007) | MedUni Vienna | institution, university |
is related to: PRECISESADS has parent organization: University of Vienna; Vienna; Austria is parent organization of: Medical University of Vienna Institute of Neurology |
SCR_005007 | SciCrunch Registry | Medical University Vienna, Medizinische Universitat Wien, Medical University of Vienna, Medizinische Universität Wien | 2026-09-26 02:19:48 | 0 | |||||||||||
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Yale School of Medicine; Connecticut; USA Resource Report Resource Website 1+ mentions |
Yale School of Medicine; Connecticut; USA (RRID:SCR_006339) | YSM | institution, university |
has parent organization: Yale University; Connecticut; USA is parent organization of: iFad is parent organization of: YPED is parent organization of: NIDDK Inflammatory Bowel Disease Genetics Consortium is parent organization of: ALFRED is parent organization of: pairedBayes is parent organization of: RNASeqBias is parent organization of: MSClust is parent organization of: pRESTO is parent organization of: Models of SHM Targeting and Substitution is parent organization of: GOArray is parent organization of: Olfactory Receptor DataBase is parent organization of: Yale School of Medicine Pharmacology is parent organization of: Btrim is parent organization of: Yale Pathology Tissue Services is parent organization of: DISCO is parent organization of: Neuroscience Gateway is parent organization of: National Mouse Metabolic Phenotyping Centers is parent organization of: Yale Cooperative Center of Excellence in Hematology is parent organization of: Yale Cooperative Center of Excellence in Hematology Animal Modeling Core is parent organization of: Yale Cooperative Center of Excellence in Hematology Imaging Core is parent organization of: Yale Cooperative Center of Excellence in Hematology Cell Preparation and Analysis Core is parent organization of: George M. O'Brien Kidney Center at Yale Mouse Genetics and Cell Line Core is parent organization of: George M. O'Brien Kidney Center at Yale Human Genetics and Clinical Research Core is parent organization of: George M. O'Brien Kidney Center at Yale Renal Physiology Core is parent organization of: George M. O'Brien Kidney Center at Yale is parent organization of: Yale Liver Center Morphology Core is parent organization of: Yale Liver Center Clinical and Translational Core is parent organization of: Yale Liver Center Cellular and Molecular Physiology Core is parent organization of: Yale Liver Center Administrative Core is parent organization of: Yale Liver Center is parent organization of: Yale School of Medicine Flow Cytometry Core Facility is parent organization of: Yale Keck Mass Spectrometry and Proteomics Resource Core Facility |
SCR_006339 | SciCrunch Registry | Yale School of Medicine, Yale University School of Medicine | 2026-09-26 02:19:49 | 1 |
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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 U24DK097771.
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