Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Soft Flow Resource Report Resource Website 1+ mentions |
Soft Flow (RRID:SCR_002599) | instrument supplier, material resource | Commercial company that develops and sells flow cytometry assay development software and analytical cytology tools. | cytometry assay development, cytology | Restricted | nlx_152464 | SCR_002599 | SciCrunch Registry | Soft Flow inc. | 2026-10-24 12:52:06 | 3 | |||||||||
|
Reliable detection of directional couplings using rank statistics Resource Report Resource Website 1+ mentions |
Reliable detection of directional couplings using rank statistics (RRID:SCR_001662) | Reliable detection of directional couplings using rank statistics | software resource, source code | Source code that allows you to calculate the different measures used in Chicharro D, Andrzejak RG (2009): Reliable detection of directional couplings using rank statistics. Physical Review E, 80, 026217. | directional coupling, time series, rank statistics, normalization, experimental signal | has parent organization: Pompeu Fabra University; Barcelona; Spain | PMID:19792241 | Free, Freely Available | nlx_153987 | SCR_001662 | SciCrunch Registry | 2026-10-24 12:52:04 | 1 | |||||||
|
EID: Exon-Intron Database Resource Report Resource Website 10+ mentions |
EID: Exon-Intron Database (RRID:SCR_002469) | EID | data or information resource, data set | Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. | eukaryote genome, exon, exon-intro, gene structure, genome splicing, intron, ortholog, fasta, gene, protein-coding gene, splice, motif, gene prediction, structure, coding region |
is listed by: OMICtools has parent organization: University of Toledo; Ohio; USA |
PMID:16772261 PMID:10592221 |
Free, Available for download, Freely available | OMICS_01886, nif-0000-02793 | http://www.utoledo.edu/med/depts/bioinfo/database.html | http://www.meduohio.edu/bioinfo/eid/, http://mcb.harvard.edu/gilbert/EID | SCR_002469 | SciCrunch Registry | The Exon-Intron Database, Exon-Intron Database | 2026-10-24 12:52:05 | 11 | ||||
|
RiVuR Resource Report Resource Website 1+ mentions |
RiVuR (RRID:SCR_001539) | RIVUR | clinical trial, resource | Multicenter, randomized, double-blind, placebo-controlled trial is designed to determine whether daily antimicrobial prophylaxis is superior to placebo in preventing recurrence of urinary tract infection (UTI) in children with vesicoureteral reflux (VUR). The basic eligibility criteria are: (1) age at randomization of at least 2 months, but less than 6 years, (2) a diagnosed first febrile or symptomatic UTI within 42 days prior to randomization that was appropriately treated, and (3) presence of Grade I-IV VUR based on voiding cystourethrogram (VCUG). Patients will be randomly assigned to treatment for 2 years with daily antimicrobial prophylaxis (trimethoprim-sulfamethoxazole) or placebo. The study is designed to recruit 600 children (approximately 300 in each treatment group) over an 18-24 month period. The primary endpoint is recurrence of UTI. In addition, patients will be evaluated for secondary endpoints related to renal scarring and antimicrobial resistance. Scarring will be determined based on renal scintigraphy by 99mTc dimercaptosuccinic (DMSA) scan. Quality of life, compliance, safety parameters, utilization of health resources, and change in VUR will be assessed periodically throughout the study. | child, antimicrobial prophylaxis, placebo, antibiotic, renal scarring, pediatric, trimethoprim-sulfamethoxazole, intervention, kidney, antibiotic resistance, young human, infant, bibliography, clinical, trimethoprim, sulfamethoxazole |
is listed by: ClinicalTrials.gov is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Vesico-ureteral reflux, Urinary tract infection | NIDDK | PMID:19570724 PMID:19018048 PMID:18076937 PMID:19018047 PMID:19086141 |
Free, Freely available | nlx_152848 | http://www.cscc.unc.edu/rivur/ | SCR_001539 | SciCrunch Registry | Randomized Intervention for Children With Vesicoureteral Reflux (RIVUR), Randomized Intervention for Children with Vesicoureteral Reflux, Randomized Intervention for Vesicoureteral Reflux | 2026-10-24 12:52:04 | 1 | |||
|
Eindhoven University of Technology; North Brabant; Netherlands Resource Report Resource Website |
Eindhoven University of Technology; North Brabant; Netherlands (RRID:SCR_003354) | TU/e | institution, university |
is parent organization of: vIST/e is parent organization of: 4TU.Datacentrum |
SCR_003354 | SciCrunch Registry | Technische Universiteit Eindhoven, TU Eindhoven, Eindhoven University of Technology | 2026-10-24 12:52:06 | 0 | |||||||||||
|
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 | 2026-10-24 12:52:08 | 74 | |||||||
|
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 | 2026-10-24 12:52:08 | 0 | ||||||||||
|
rsync Resource Report Resource Website 1+ mentions |
rsync (RRID:SCR_003113) | software resource, source code | Software that provides rapid incremental file transfer. | file transfer |
is used by: studyforrest.org has parent organization: Samba |
Free, Available for download, Freely available | nlx_156711 | SCR_003113 | SciCrunch Registry | 2026-10-24 12:52:06 | 7 | |||||||||
|
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 | 2026-10-24 12:52:08 | 0 | ||||||||||||
|
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 | 2026-10-24 12:52:08 | 2 | ||||||
|
HSPH Trace Metals Laboratory Resource Report Resource Website 1+ mentions |
HSPH Trace Metals Laboratory (RRID:SCR_002819) | HSPS Trace Metals Laboratory | access service resource, core facility, service resource | Core facility that provides metals analytical capabilities to biomedical and non-biomedical researchers and serves as a source for study design consultation and sample QA/QC requirements. The transport, fate, exposure, and toxic effects of heavy metals is a primary focus of research at the Center. It operates as a modified fee-for-service laboratory. Researchers have the option of having the samples run by the Service staff, or of receiving instruction (for themselves or a doctoral or post doctoral trainee) on how to operate the analytical equipment and analyze their own samples. Both options have associated fees and, as with other services, facility access funds can be requested internal or external services when individual grant support is not yet available. | transport, fate, exposure, toxicity, heavy metal |
is listed by: Eagle I has parent organization: Harvard T.H. Chan School of Public Health |
Restricted | nlx_156296 | http://www.hsph.harvard.edu/niehs/member-resources-2/ihfsc/metals-service/, http://search.sph.harvard.edu/research/niehs/facility-cores/trace-metals-lab/ | https://apps.sph.harvard.edu/publisher/upload/research/niehs/facility-cores/trace-metals-lab/ | SCR_002819 | SciCrunch Registry | Harvard NIEHS Center for Environmental Health Trace Metals Lab, Trace Metals Laboratory (HSPH) | 2026-10-24 12:52:05 | 1 | |||||
|
HS3D - Homo Sapiens Splice Sites Dataset Resource Report Resource Website 1+ mentions |
HS3D - Homo Sapiens Splice Sites Dataset (RRID:SCR_002939) | HS3D | data or information resource, data set | Data set of Homo Sapiens Exons, Introns and Splice regions extracted from GenBank Rel.123 with an aim of giving standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries. Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation). 3799+3799 donor and acceptor sites, as windows of 140 nucleotides around each splice site have been extracted. After discarding sequences not including canonical GTAG junctions (65+74), including insufficient data (not enough material for a 140 nucleotide window) (686+589), including not AGCT bases (29+30), and redundant (218+226) there are 2796+ 2880 windows. Finally, there are 271,937 + 332,296 windows of false splice sites, selected by searching canonical GTAG pairs in not splicing positions. The false sites in a range of +/- 60 from a true splice site are marked as proximal. | human genome, splice, exon, intron, region, gene, dna, nucleotide, splice region | is related to: GenBank | Free, Available for download, Freely available | nif-0000-02988 | SCR_002939 | SciCrunch Registry | Homo Sapiens Splice Sites Dataset, HS3D (Homo Sapiens Splice Sites Dataset) | 2026-10-24 12:52:05 | 7 | |||||||
|
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 | 2026-10-24 12:52:07 | 7 | |||||||||||||
|
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 | 2026-10-24 12:52:07 | 6 | |||||
|
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 | 2026-10-24 12:52:06 | 0 | |||||||
|
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 | 2026-10-24 12:52:09 | 0 | |||||||||||
|
Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra Resource Report Resource Website |
Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra (RRID:SCR_004315) | software resource, source code | Charge Czar is a software tool that uses a support vector machine to discriminate between +2- and +3-charged tandem mass spectra, with the goal of reducing database search time by eliminating the need to search twice with each spectrum. Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded after you have agreed to the license agreement. Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current charge-state-determination algorithms only discriminate singly- from multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiply-charged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra. | has parent organization: University of Washington; Seattle; USA | PMID:16447975 | nlx_32529 | SCR_004315 | SciCrunch Registry | ChargeCzar, Charge Czar | 2026-10-24 12:52:07 | 0 | |||||||||
|
Mouse Genome Informatics Transgenes Resource Report Resource Website 1+ mentions |
Mouse Genome Informatics Transgenes (RRID:SCR_003468) | MGI Transgene | data or information resource, data set |
Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available. Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice. |
transgene, allele, phenotype |
is used by: NIF Data Federation is related to: Integrated Manually Extracted Annotation has parent organization: Mouse Genome Informatics (MGI) |
Acknowledgement requested, Non-commercial, Commercial with permission, Copyrighted | nif-0000-34000 | SCR_003468 | SciCrunch Registry | 2026-10-24 12:52:06 | 3 | ||||||||
|
ALLBUS - German General Social Survey Resource Report Resource Website |
ALLBUS - German General Social Survey (RRID:SCR_003588) | ALLBUS | data or information resource, data set | Data set of up-to-date data on attitudes, behavior, and social structure in Germany. Every two years since 1980 a representative cross section of the population is surveyed using both constant and variable questions. The ALLBUS data become available to interested parties for research and teaching as soon as they are processed and documented. | social sciences, attitude, behavior, social structure, germany | is listed by: re3data.org | nlx_157750 | SCR_003588 | SciCrunch Registry | ALLBUS (Allgemeine Bev?lkerungsumfrage der Sozialwissenschaften) (German General Social Survey), German General Social Survey, Allgemeine Bev?lkerungsumfrage der Sozialwissenschaften | 2026-10-24 12:52:06 | 0 | ||||||||
|
Segtools Resource Report Resource Website 1+ mentions |
Segtools (RRID:SCR_004394) | software resource, source code | Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another. | has parent organization: University of Washington; Seattle; USA | PMID:22029426 | nlx_40271 | SCR_004394 | SciCrunch Registry | 2026-10-24 12:52:07 | 5 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
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.
Email: info_at_ dknet.org
