Searching the RRID Resource Information Network
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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BEBaC Resource Report Resource Website |
BEBaC (RRID:SCR_000621) | BEBaC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities. | linux, bayesian |
is listed by: OMICtools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:22406836 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01440 | SCR_000621 | Bayesian estimation of bacterial communities | 2026-02-14 01:59:46 | 0 | ||||||
|
FlipFlop Resource Report Resource Website |
FlipFlop (RRID:SCR_000625) | software resource | Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. | standalone software, unix/linux, mac os x, windows, r, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24813214 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04028, biotools:flipflop | https://bio.tools/flipflop | SCR_000625 | flipflop - Fast lasso-based isoform prediction as a flow problem | 2026-02-14 01:59:50 | 0 | ||||||
|
Australian Wool Innovation Limited Resource Report Resource Website |
Australian Wool Innovation Limited (RRID:SCR_000775) | commercial organization | Company focused on animal welfare and pest prevention in the wool industry. | wool, innovation, animal, health, welfare, prevention, parasite, science, resource, weed, pest, feral predator, breeding | nif-0000-30047 | http://www.wool.com.au/LivePage.aspx?pageId=116 | SCR_000775 | AWI | 2026-02-14 01:59:50 | 0 | |||||||||
|
GMcloser Resource Report Resource Website 1+ mentions |
GMcloser (RRID:SCR_000646) | GMcloser | software resource | Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:26261222 | Free, Available for download, Freely available | biotools:gmcloser, OMICS_00042 | https://bio.tools/gmcloser | SCR_000646 | Gmcloser - Closing the gaps in scaffolds with preassembled contigs | 2026-02-14 01:59:50 | 3 | |||||
|
detecttd Resource Report Resource Website |
detecttd (RRID:SCR_000681) | detecttd | software resource | Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone. | tandem duplication, sequencing read, python, next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00315 | SCR_000681 | detecttd - Tool to detect tandem duplications in NGS reads | 2026-02-14 01:59:48 | 0 | |||||||
|
FastUniq Resource Report Resource Website 1+ mentions |
FastUniq (RRID:SCR_000682) | software resource | A software tool for removal of de novo duplicates in paired short DNA sequences. | de novo, dna, sequence, duplicate, |
is listed by: OMICtools has parent organization: SourceForge |
DOI:10.1371/journal.pone.0052249 | Free, Available for download, Freely available | OMICS_01044 | SCR_000682 | 2026-02-14 01:59:51 | 3 | ||||||||
|
Sequencing Analysis Software Resource Report Resource Website 1+ mentions |
Sequencing Analysis Software (RRID:SCR_000718) | Sequencing Analysis Software | software resource | A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends. | basecall, capillary dna, quality control, low-quality sequence ends | is listed by: OMICtools | Restricted | OMICS_01814 | SCR_000718 | 2026-02-14 01:59:52 | 1 | ||||||||
|
Stanford University Psychiatry and Behavioral Sciences Resource Report Resource Website |
Stanford University Psychiatry and Behavioral Sciences (RRID:SCR_000719) | university | A Stanford-affiliated organization which is primarily concerned with the study and treatment of sleep disorders, the treatment of psychological illnesses, and the training of medical students, residents and research fellows in psychiatry and sleep medicine. | stanford, sleep disorder, psychiatry, medical, psychological illness, research, medicine | nif-0000-02073 | SCR_000719 | Stanford | 2026-02-14 01:59:49 | 0 | ||||||||||
|
Scripps Women's College, Neuroscience Department Resource Report Resource Website |
Scripps Women's College, Neuroscience Department (RRID:SCR_000717) | university | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A neuroscience program that prepares the student for graduate work in biology, psychology, neuroscience, or preparation for medical school or a career in the health services. | neuroscience, psychology, biology, health sciences, medical, services, graduate | has parent organization: Scripps College; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02059 | SCR_000717 | Scripps College Neuroscience | 2026-02-14 01:59:49 | 0 | ||||||||
|
clipcrop Resource Report Resource Website |
clipcrop (RRID:SCR_000678) | software resource | Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files. | structural variation, detecting structural variations, soft-clipping information, SAM files, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22373054 | Free, Available for download, Freely available | biotools:clipcrop, OMICS_00310 | https://bio.tools/clipcrop | SCR_000678 | ClipCrop | 2026-02-14 01:59:48 | 0 | ||||||
|
Americans for Medical Progress Resource Report Resource Website |
Americans for Medical Progress (RRID:SCR_000711) | AMP | nonprofit organization | A non-profit charity dedicated to providing education about animal research for the purpose of protecting medical and scientific progress. The organization seeks to provide accurate and incisive information to foster a balanced public debate on animal research issues. They work to do outreach by distributing timely and relevant news, information and analysis about animal rights extremism to the research community. | animal, research, issue, extremism, education, progress, debate | Crossref funder ID: 100005411, grid.468272.d, nif-0000-00456, Wikidata: Q4745618, ISNI: 0000 0004 4659 713X | https://ror.org/05xxn0r26 | SCR_000711 | 2026-02-14 01:59:49 | 0 | |||||||||
|
TriageTools Resource Report Resource Website |
TriageTools (RRID:SCR_000675) | TriageTools | software resource | A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. | matlab, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23408855 | Free, Available for download, Freely available | biotools:triagetools, nlx_156740 | https://bio.tools/triagetools | SCR_000675 | 2026-02-14 01:59:48 | 0 | ||||||
|
Oregon State University College of Pharmacy Resource Report Resource Website |
Oregon State University College of Pharmacy (RRID:SCR_000715) | university | The college of pharmacy at Oregon State University that offers professional education in pharmacy. The foundational goals are to provide professional education, foster research to contribute to public health initiatives and promote safe and affordable medication access. | pharmacy, pharmaceutical, professional, education, public health, access, medication, drugs | nif-0000-02038 | SCR_000715 | Oregon State | 2026-02-14 01:59:49 | 0 | ||||||||||
|
VarB Resource Report Resource Website |
VarB (RRID:SCR_000671) | VarB | software resource | A variation browsing and analysis tool for variants derived from next-generation sequencing data. | variant, next-generation sequencing, polymorphism, c++ | is listed by: OMICtools | PMID:22976080 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00898 | SCR_000671 | 2026-02-14 01:59:51 | 0 | |||||||
|
BC Cancer Agency Resource Report Resource Website 1+ mentions |
BC Cancer Agency (RRID:SCR_004201) | BCCA | institution | A portal that provides a province-wide, population-based cancer control program for the residents of British Columbia and the Yukon. The BC Cancer Agency''s mandate covers the spectrum of cancer care, from prevention and screening, to diagnosis, treatment, and through to rehabilitation. The BC Cancer Agency''s mandate is driven by a three-fold mission: 1. To reduce the incidence of cancer; 2. To reduce the mortality rate of people with cancer; 3. To improve the quality of life of people living with cancer. This mission drives everything we do, including providing screening, diagnosis and care, setting treatment standards, and conducting research into causes of, and cures for, cancer. The BC Cancer Agency operates five regional cancer centers, providing assessment and diagnostic services, chemotherapy, radiation therapy, and supportive care. Each of the BC Cancer Agency''s centers delivers cancer treatment based on provincial standards and guidelines established by the Agency. We work in partnership with communities to provide a network of chemotherapy clinics so patients can receive care closer to home. Research is an essential part of the BC Cancer Agency''s mission to not only find the causes of cancer, but to find better treatments for prolonged life and better quality of life. With direct links between the BC Cancer Agency''s physicians and researchers at our five centers, the Deeley Research Centre (located in Victoria) and the BC Cancer Agency''s Research Centre (located in Vancouver), we can quickly translate new discoveries into clinical applications. The BC Cancer Agency''s Research Centre includes eight specialty laboratories including the Genome Sciences Centre, and the Terry Fox Laboratory. The BC Cancer Foundation raises funds for cancer research and enhancements to care at the BC Cancer Agency. |
is related to: BC Cancer Foundation is parent organization of: cisRED: cis-regulatory element is parent organization of: British Columbia Gynaecologic Tissue Bank is parent organization of: British Columbia Tumour Tissue Repository is parent organization of: Spark is parent organization of: ALEA is parent organization of: APOLLOH is parent organization of: British Columbia Breast Cancer Tumour Bank is parent organization of: JointSNVMix is parent organization of: mutationSeq is parent organization of: Mouse Gene Expression at the BC Cancer Agency is parent organization of: C. elegans Resources is parent organization of: BCCA Cancer Drug Manual is parent organization of: flowCL is parent organization of: flowBin |
Cancer | BC Cancer Foundation | ISNI: 0000 0001 0702 3000, Wikidata: Q4835275, grid.248762.d, nlx_143635, Crossref funder ID: 501100005614 | https://ror.org/03sfybe47 | SCR_004201 | British Columbia Cancer Agency | 2026-02-14 02:00:57 | 3 | ||||||
|
Echelon Biosciences Resource Report Resource Website 50+ mentions |
Echelon Biosciences (RRID:SCR_004169) | EBI | commercial organization | An Antibody supplier | nlx_152350 | SCR_004169 | Echelon Biosciences Inc., Echelon Biosciences Incorporated | 2026-02-14 02:00:55 | 75 | ||||||||||
|
OBO Relation Ontology Resource Report Resource Website |
OBO Relation Ontology (RRID:SCR_004285) | OBO REL, RO | data or information resource, ontology, controlled vocabulary | The OBO Relation Ontology is an ontology of core relations for use by OBO Foundry ontologies. To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena. The OBO Relation ontology is undergoing substantial changes: * Core domain-independent relations will live in BFO * Biology specific relations (defined in terms of core relations) will live in RO |
is related to: African Population Ontology has parent organization: OBO |
PMID:15892874 | nlx_33226 | SCR_004285 | Relation Ontology, OBO RO | 2026-02-14 02:00:57 | 0 | ||||||||
|
MSG Resource Report Resource Website 1+ mentions |
MSG (RRID:SCR_004161) | MSG | software resource | A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. | next generation sequencing, genotyping, genetic mapping, ancestry, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
PMID:21233398 | OMICS_01551 | SCR_004161 | Multiplexed shotgun genotyping, Multiplexed shotgun genotyping (MSG), MSG: Multiplexed Shotgun Genotyping | 2026-02-14 02:00:41 | 2 | |||||||
|
MicroBrightfield, Inc. Resource Report Resource Website 50+ mentions |
MicroBrightfield, Inc. (RRID:SCR_004314) | MBF | commercial organization | A provider for commercial products for analyzing neuronal morphology, stereology, etc. | neurolucida, neuronal morphology, neuronal stereology | Organization | Wikidata: Q6714719, grid.421345.5, nif-0000-00110 | https://ror.org/02zynam48 | SCR_004314 | mbf Bioscience, MicroBrightfield | 2026-02-14 02:00:57 | 54 | |||||||
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University of Pennsylvania; Philadelphia; USA Resource Report Resource Website 1+ mentions |
University of Pennsylvania; Philadelphia; USA (RRID:SCR_004275) | UPenn, Penn State | university | University of Pennsylvania is private Ivy League research university located in University City neighborhood of Philadelphia, Pennsylvania. Established in 1740, UPenn has 4 undergraduate schools and 12 graduate schools. | undergraduate, graduate, master's, doctoral, phD, institution, university |
uses: Research Accelerator is affiliated with: Diabetes Research Centers is related to: International AMD Genetics Consortium is related to: Clinical and Translational Science Awards Consortium is related to: Cooperative Human Tissue Network is related to: PIVOT software is related to: Urinary Stone Disease Research Network is parent organization of: Penn Cell and Developmental Biology Zebrafish Core is parent organization of: Penn Clinical Research Computing Unit is parent organization of: Penn Community Outreach Using Health System Informatics Core is parent organization of: Penn Hippocampus Atlas is parent organization of: NIH/Merial Veterinary Scholars Program is parent organization of: Penn Diabetes Research Center Mouse Phenotyping Physiology and Metabolism Core is parent organization of: Penn Research Instrumentation Shop is parent organization of: Penn Small Animal Imaging Facility: PET/SPECT/CT Sub-Core is parent organization of: Penn Translational Biomarker Core is parent organization of: Diffusion Tensor Imaging ToolKit is parent organization of: ApiDots is parent organization of: Hierarchical Attribute Matching Mechanism for Elastic Registration is parent organization of: ITK-SNAP is parent organization of: Database of Transcribed Sequences is parent organization of: PennCNV is parent organization of: Brain lesion segmentation tool using SVM is parent organization of: RNA Abundance Database is parent organization of: Cognitive Electrophysiology Data Portal is parent organization of: ANTS - Advanced Normalization ToolS is parent organization of: Atrophy Simulation Package is parent organization of: 3DViewnix is parent organization of: miRGen is parent organization of: OrthoMCL DB: Ortholog Groups of Protein Sequences is parent organization of: University of Pennsylvania School of Medicine Penn Diabetes Research Center Pancreatic Islet Cell Biology Core Facility is parent organization of: BRAID is parent organization of: AHEAD is parent organization of: Penn Laser Confocal Microscope Core is parent organization of: DRAMMS is parent organization of: fMRI Grocer is parent organization of: Penn Automated Claims and Medical Record Databases is parent organization of: CHOP Biostatistics and Data Management Core is parent organization of: CHOP CTRC Behavioral Neurosciences Core is parent organization of: CHOP CTRC Cardiovascular Imaging Core is parent organization of: CHOP CTRC Nutrition Core Nutrition Assessment is parent organization of: CHOP CTRC Ophthalmology Core is parent organization of: CHOP Clinical Trials Office is parent organization of: CHOP Flow Cytometry Core Laboratory is parent organization of: CHOP Human Embryonic stem cell/induced pluripotent stem cell Core is parent organization of: CHOP Nucleic Acid/Protein Core is parent organization of: CHOP Pathology Core Laboratories is parent organization of: Penn/CHOP CTRC Informatics Services Core is parent organization of: Monell Behavioral and Physiological Phenotyping Core is parent organization of: Monell Chemosensory Receptor Signaling Core is parent organization of: Monell Genotyping and DNA/RNA Analysis Core is parent organization of: Monell Histology and Cellular Localization Core is parent organization of: Penn Mass Spectrometry Molecular Profiling Core is parent organization of: Penn BioMechanics Core Facility is parent organization of: Penn Biological Chemistry Resource Center is parent organization of: Penn Cancer Histology Core is parent organization of: Penn Cell Center Services Facility is parent organization of: Penn Cell Center Stockroom is parent organization of: Penn Cell and Developmental Biology Microscopy Core is parent organization of: Penn Chemistry NMR Facility is parent organization of: Penn Clinical Cell and Vaccine Production Facility is parent organization of: Penn Community Engagement and Research Core is parent organization of: Penn/CHOP CTRC Bionutrition Research Core Dietary Assessment is parent organization of: Penn Electron Microscopy Resource Laboratory is parent organization of: Penn Flow Cytometry and Cell Sorting Resource Laboratory is parent organization of: Penn Investigational Drug Service is parent organization of: Penn Gene Targeting Service is parent organization of: University of Pennsylvania Molecular Profiling Facility is parent organization of: Penn High-Throughput Sequencing Facility is parent organization of: University of Pennsylvania High-performance Computing is parent organization of: Penn Histology and Gene Expression Core is parent organization of: Penn Human Immunology Core is parent organization of: Penn Interventional Radiology Animal Catheter Lab is parent organization of: Penn Mass Spectrometry Facility is parent organization of: University of Pennsylvania Molecular Profiling Facility Bioinformatics is parent organization of: Penn NBIC Probe Facility is parent organization of: Penn Neurobehavior Testing Core is parent organization of: Penn Next-Generation Sequencing Core is parent organization of: Penn Proteomics and Systems Biology Core is parent organization of: Penn Diabetes Research Center Radioimmunoassay and Biomarkers Core Facility is parent organization of: Penn Regional Nanotechnology Facility is parent organization of: Penn Small Animal Imaging Facility is parent organization of: Penn Small Animal Imaging Facility: MRI/MRS Sub-Core is parent organization of: Penn Small Animal Imaging Facility: Optical/Bioluminescence Sub-Core is parent organization of: Penn Small Animal Imaging Facility: Ultrasound Sub-Core is parent organization of: Pennsylvania University Perelman School of Medicine Stem Cell and Xenograft Core Facility is parent organization of: Penn Diabetes Research Center Transgenic and Chimeric Mouse Core Facility is parent organization of: University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Vector Core Facility is parent organization of: Penn/CHOP CTRC Research Nurse Core is parent organization of: Penn/CHOP CTRC Sleep Core is parent organization of: Penn/CHOP CTRC Study Design and Biostatistics Core is parent organization of: Penn/CHOP CTRC Translational Core Laboratories is parent organization of: Penn/CHOP Office of Human Subject Recruitment and Protection is parent organization of: TESS: Transcription Element Search System is parent organization of: CoRAL - Classification of RNAs by Analysis of Length is parent organization of: University of Pennsylvania Labs and Facilities is parent organization of: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA is parent organization of: SBIA is parent organization of: TalkBank is parent organization of: IsoformEx is parent organization of: Neuron-C is parent organization of: GIMME is parent organization of: DTI-TK is parent organization of: Referral Center for Animal Models of Human Genetic Diseases is parent organization of: MAJIQ is parent organization of: ReBATE is parent organization of: PennAI is parent organization of: ITK-SNAP is parent organization of: Pharmacogenetics of Nicotine Addiction Treatment is parent organization of: 4D Genome is parent organization of: AsPredicted is parent organization of: HistoloZee is parent organization of: University of Pennsylvania School of Veterinary Medicine Center for Host Microbial Interactions Core Facility is parent organization of: University of Pennsylvania Electronic Phenotyping Resource Core Facility is parent organization of: University of Pennsylvania Penn Vet Imaging Core Facility is parent organization of: University of Pennsylvania School of Dental Medicine Tissue Processing Laboratory Core Facility is parent organization of: University of Pennsylvania Institute for RNA Innovation Engineered mRNA and Targeted Nanomedicine Core Facility is parent organization of: University of Pennsylvania Institute for Immunology and Immune Health I3H Core Facility is parent organization of: University of Pennsylvania Institute for RNA Innovation Targeting Core Facility is parent organization of: University of Pennsylvania Bollinger Digital Fabrication Laboratory Core Facility |
Wikidata:Q49117, SCR_022445, grid.25879.31, ISNI:0000 0004 1936 8972, nlx_24937, Crossref funder ID:100006920 | https://ror.org/00b30xv10 | SCR_004275 | University of Pennsylvania | 2026-02-14 02:00:38 | 5 |
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