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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Astrocyte Reactivity RNA-Seq Browser Resource Report Resource Website 1+ mentions |
Astrocyte Reactivity RNA-Seq Browser (RRID:SCR_015033) | data or information resource, database | Database containing information about RNA-sequencing and astrocyte reactivity. Searching a gene through this engine provides differential expression data for various experimental conditions. | astrocyte, glia, reactivity, rna-seq, search engine | has parent organization: University of California Los Angeles Department of Neurobiology | NIH NS057624; NIH NS084030; NIH P30 NS062691; NIH NS060677; NIH MH099559A; NIH MH104069; Dr. Miriam and Sheldon G. Adelson Medical Foundation ; Wings for Life |
PMID:27027288 | Public | SCR_015033 | SciCrunch Registry | 2026-10-17 01:35:23 | 3 | ||||||||
|
Embassy-domsearch Resource Report Resource Website |
Embassy-domsearch (RRID:SCR_016086) | software resource, software toolkit, source code | Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt. | dhf, daf, redundancy, protein, domain, psi-blast, uniprot, molecular, biology |
is used by: RAVEN is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/embassy-domsearch/ | SCR_016086 | SciCrunch Registry | 2026-10-17 01:33:37 | 0 | |||||||||
|
WILD Resource Report Resource Website |
WILD (RRID:SCR_016240) | analysis service resource, material analysis service, production service resource, service resource | Service that distinguishes Isoleucine and Leucine using mass spectrometry experiments. | isoleucine, leucine, mass, spectrometry, ion, chemical, biochemistry | Commercially available, Free consultation | SCR_016240 | SciCrunch Registry | WILD (W-ion Isoleucine Leucine Determination), W-ion Isoleucine Leucine Determination | 2026-10-17 01:33:40 | 0 | ||||||||||
|
Glycan Mass Spectral Database (GMDB) Resource Report Resource Website |
Glycan Mass Spectral Database (GMDB) (RRID:SCR_014667) | GMDB | data or information resource, database | A multistage tandem mass spectral database using a variety of structurally defined glycans. It provides tools for glycomics research that enable users to identify glycans by spectral matching. The database stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans. | glycomics, database, metagenomics, glycan, mass, spectral matching, tandem mass spectra | is listed by: Metabolomics Workbench | New Energy and Industrial Technology Development Organization ; Ministry of Education Culture Sports Science and Technology MEXT ; Tsukuba Advanced Computing Center of the National Institute of Advanced Industrial Science and Technology |
SCR_014667 | SciCrunch Registry | Glycan Mass Spectral Database | 2026-10-17 01:35:22 | 0 | ||||||||
|
Mass Spectral Library Resource Report Resource Website 10+ mentions |
Mass Spectral Library (RRID:SCR_014668) | data or information resource, database | A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals. | library, database, spectra, mass spectrometry, metabolomics, metabolites, protein, lipid, contaminant | is listed by: Metabolomics Workbench | Available with the NIST MS Search Program for Windows | SCR_014668 | SciCrunch Registry | 2026-10-17 01:33:38 | 21 | ||||||||||
|
SEARCHBreast Resource Report Resource Website 1+ mentions |
SEARCHBreast (RRID:SCR_014826) | biomaterial supply resource, material resource, tissue bank | Database and repository of tissues relating to mouse models of breast cancer. Users can search and share models, and members can enter details of available material to share on a collaborative basis. | breast cancer, database, tissue bank, in vivo, in vitro, mouse model | PMID:26062499 | Open to any UK based breast cancer researcher who uses in in vivo experimentation | SCR_014826 | SciCrunch Registry | 2026-10-17 01:34:17 | 8 | ||||||||||
|
Datasets2Tools Resource Report Resource Website 1+ mentions |
Datasets2Tools (RRID:SCR_016174) | data or information resource, database | Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools. | biomedical, digital, bioinformatics, dataset, rna seq, computation, microarray, proteomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Public, Freely available | biotools:datasets2tools | https://bio.tools/datasets2tools | SCR_016174 | SciCrunch Registry | 2026-10-17 01:35:26 | 1 | ||||||||
|
cwltool Resource Report Resource Website 10+ mentions |
cwltool (RRID:SCR_015528) | software resource, software toolkit, source code | Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host. | language, reference implementation, python |
uses: Python Programming Language is listed by: Debian is listed by: OMICtools |
DOI:10.6084/m9.figshare.3115156.v2 | Available for download | OMICS_28977 | https://sources.debian.org/src/cwltool/ | SCR_015528 | SciCrunch Registry | CWLtool, Common Workflow Language Tool | 2026-10-17 01:35:24 | 25 | ||||||
|
Soma-Segmentation Resource Report Resource Website 1+ mentions |
Soma-Segmentation (RRID:SCR_015649) | algorithm resource, software resource, source code | Source code for a soma segmentation method suitable for datasets with touching soma distributions. The method contains three main parts: soma detection based on DT and local maximum searching and refining; an improved Rayburst sampling algorithm for isolated and touching soma surface detection; and ellipsoid fitting to generate the segmentation results. | soma, segmentation method, touching soma distribution, rayburst sampling algorithm, soma detection, matlab | uses: MATLAB | Free, Available for download | SCR_015649 | SciCrunch Registry | 2026-10-17 01:33:39 | 1 | ||||||||||
|
UManitoba - JHU Functionally Defined Human White Matter Atlas Resource Report Resource Website 1+ mentions |
UManitoba - JHU Functionally Defined Human White Matter Atlas (RRID:SCR_015525) | atlas, data or information resource | Probabilistic atlas of human white matter tracts/regions underlying several well-known resting state brain networks. The atlas includes group probability maps for each network, as well as each individual tract that are aligned to both the SPM and MRIStudio ICBM templates. | white matter, dti tractography, resting state brain network, group probability map |
works with: MRI Studio works with: SPM works with: 3D Slicer |
PMID:26578930 | Acknowledgement requested, Freely available, Available for download | SCR_015525 | SciCrunch Registry | UManitoba JHU Functionally Defined Human White Matter Atlas, UManitoba-JHU Functionally-Defined Human White Matter Atlas | 2026-10-17 01:33:37 | 1 | ||||||||
|
Reefgenomics Resource Report Resource Website 10+ mentions |
Reefgenomics (RRID:SCR_015009) | data or information resource, database | Database for marine genomics data. Users can access genomics datasets from various organisms as well as carry out BLAST and submit genomics information of their own. Data sets include coral, aiptasia, sponges, and sybiodinium. | marine genomics, genomics database, blast | has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia | DOI:10.1093/database/baw152 | Available to the research community, The community can contribute to this resource | SCR_015009 | SciCrunch Registry | reefgenomics.org | 2026-10-17 01:33:37 | 43 | ||||||||
|
Chemical Translation Service Resource Report Resource Website 10+ mentions |
Chemical Translation Service (RRID:SCR_014681) | CTS | data or information resource, database, service resource | A translation service which contains a registry of pubicly available chemical information such as structures, chemical names, chemical synonyms, database identifiers, molecular masses, XlogP and proton-donor/acceptor data for compound-specific, structure-based cross references. It offers single ID conversion, batch ID conversion, InChI code conversion, and other services. | translation service, chemical translation, metabolomics, metabolomics tool, chemical properties, chemical structure, compound, chemical registry, cross reference |
is listed by: Metabolomics Workbench has parent organization: Metabolomics Fiehn Lab |
Available to public, A web GUI is used and a soap-based application-programming interface was implemented for automated access | SCR_014681 | SciCrunch Registry | Chemical Translation Service (CTS) | 2026-10-17 01:33:38 | 25 | ||||||||
|
Mamit tRNA Resource Report Resource Website 1+ mentions |
Mamit tRNA (RRID:SCR_015493) | data or information resource, database | Compilation of mammalian mitochondrial tRNA genes. Sequences are classified into families according to the amino acid specificity of the different tRNAs as defined by the anticodon triplets. Each sequence is displayed linearly with color codes indicating secondary structural domains. | mammal mitochondria dna, mammal mitochondria gene, mammal mitochondria trna | PMID:11073213 | SCR_015493 | SciCrunch Registry | Mamit-tRNA | 2026-10-17 01:33:39 | 2 | ||||||||||
|
CATALYSTLite Resource Report Resource Website |
CATALYSTLite (RRID:SCR_017126) | analysis service resource, data analysis service, production service resource, service resource | Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package. | interactive, Shiny, website, application, interface, mass, cytometry, data, processing, pipeline |
is used by: CATALYST is related to: Bioconductor has parent organization: University of Zurich; Zurich; Switzerland |
Free, Freely available | SCR_017126 | SciCrunch Registry | 2026-10-17 01:34:19 | 0 | ||||||||||
|
CaspBase Resource Report Resource Website 1+ mentions |
CaspBase (RRID:SCR_018975) | data or information resource, database | Database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Tool to rapidly disseminate organized caspase sequence data. Includes all animal species with currently available annotated genomes in NCBI genome database. Manually curated and not curated sequences are available to download. | Caspase sequences, curated data, caspase, caspase functional divergence, ancestral sequence inference, data analysis, dataset |
is related to: NCBI Genome is related to: NCBI |
PMID:30076665 | Free, Available for download, Freely available | SCR_018975 | SciCrunch Registry | Caspase Sequence Database | 2026-10-17 01:33:42 | 2 | ||||||||
|
Genes, Genome Features and Maps Resource Report Resource Website 1+ mentions |
Genes, Genome Features and Maps (RRID:SCR_017524) | data or information resource, database | Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models. | Data, mouse, gene, DNA, segment, cytogenetic, marker, MGI, genome, feature, sequenced, genomic, map, expression, disease, model | Free, Freely available | SCR_017524 | SciCrunch Registry | 2026-10-17 01:33:41 | 6 | |||||||||||
|
Phenotypes and Mutant Alleles Resource Report Resource Website 10+ mentions |
Phenotypes and Mutant Alleles (RRID:SCR_017523) | data or information resource, database, service resource | Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes. | MGI, phenotype, human, disease, analysis, model, genetically, engineered, mutation, strain, specific, phenotype, data | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017523 | SciCrunch Registry | Phenotypes, Alleles & Disease Models | 2026-10-17 01:35:30 | 13 | |||||||||
|
TransmiR Resource Report Resource Website 100+ mentions |
TransmiR (RRID:SCR_017499) | data or information resource, database | Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data. | Transcription, factor, miRNA, regulation, manually, curated, TF-miRNA, ChIPseq, derived, TF-miRNA, data, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
Restricted | biotools:transmir | https://bio.tools/transmir/ | SCR_017499 | SciCrunch Registry | TransmiR v2.0 | 2026-10-17 01:33:41 | 123 | |||||||
|
Predomics Resource Report Resource Website 1+ mentions |
Predomics (RRID:SCR_017415) | software application, software resource, source code | Software package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data. | Metagenomic, data, discover, predictive, signature, unprecedented, interpretability, supervised, learning, ternary, coefficient | Assistance Publique-Hôpitaux de Paris Contrat d’interface chercheurs 2015-2018; EU-FP7 HEALTH-F4-2012-305312; French National Agency |
DOI:10.1101/409144 | Free, Available for download, Freely available | SCR_017415 | SciCrunch Registry | 2026-10-17 01:33:38 | 1 | |||||||||
|
Journal Citation Reports Resource Report Resource Website 1+ mentions |
Journal Citation Reports (RRID:SCR_017656) | JCR | data or information resource, database, service resource | Web tool with systematic, objective means to critically evaluate journals, with quantifiable, statistical information based on citation data. Provides information about academic journals in natural sciences and social sciences, including impact factors in database integrated with Web of Science. Sourced from Web of Science Core Collection,citation index on Web of Science platform. | Journal, citation, report, imapct, factor, Web of Science, index, frequency, article, importance | Free, Freely available | SCR_017656 | SciCrunch Registry | 2026-10-17 01:33:41 | 6 |
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
