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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Brain Gene Expression Analysis toolbox Resource Report Resource Website 1+ mentions |
Brain Gene Expression Analysis toolbox (RRID:SCR_017438) | data analysis software, data processing software, software application, software resource | Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain. | Quantitative, analysis, digitized, brain, gene, expression, data, Allen Atlas, adult, mouse, brain, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB is related to: Allen Institute for Brain Science works with: Allen Mouse Brain Reference Atlas |
Free, Available for download, Freely available | SCR_017438 | SciCrunch Registry | , Brain, Gene, Expression, Analysis, toolbox | 2026-09-19 12:55:17 | 1 | |||||||||
|
COVID-19 and Coronavirus plasmids and resources Resource Report Resource Website 1+ mentions |
COVID-19 and Coronavirus plasmids and resources (RRID:SCR_018347) | catalog, data or information resource, database | Collections of Addgene plasmids, open access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists. Ordering or depositing plasmids related to COVID-19 research. | Plasmid, COVID-19, SARS-CoV-2 plasmid, plasmid order, Adddgene, COVID-19 plasmid repository, COVID-19 related article, COVID-19 related protocol, COVID-19 resource collection, data | COVID-19 | Free, Freely available | SCR_018347 | SciCrunch Registry | 2026-09-19 12:55:18 | 1 | ||||||||||
|
Fitness Browser Resource Report Resource Website 1+ mentions |
Fitness Browser (RRID:SCR_018981) | data access protocol, data or information resource, software resource, web service | Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function. | Genome browser, bacteria, mutant phenotype, bacterial genes, unknown function, data | has parent organization: University of California at Berkeley; Berkeley; USA | NCRR S10 RR027303; NCRR S10 RR029668; NIH Office of the Director OD018174; Office of Science of the US Department of Energy |
PMID:29769716 | Free, Freely available | SCR_018981 | SciCrunch Registry | 2026-09-19 12:55:18 | 9 | ||||||||
|
cRAP protein sequences Resource Report Resource Website 100+ mentions |
cRAP protein sequences (RRID:SCR_018187) | cRAP | data or information resource, data repository, database, service resource, storage service resource | List of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. List is based on analysis of current version of GPMDB, as well as suggestions by users. Current version of cRAP in FASTA format can be obtained from the GPM FTP site. | Protein, collection, proteomic experiment, protein sample, contamination, Global Proteome Machine Data Base, data repository, data, FASEB list | THIS RESOURCE IS NO LONGER IN SERVICE | ftp://ftp.thegpm.org/fasta/cRAP | SCR_018187 | SciCrunch Registry | common Repository of Adventitious Proteins | 2026-09-19 12:55:17 | 198 | ||||||||
|
Loupe Browser Resource Report Resource Website 100+ mentions |
Loupe Browser (RRID:SCR_018555) | data analysis software, data processing software, software application, software resource | Desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Used to interrogate different views of 10x data to gain insights into underlying biology. | Interactive visualization, data analysis, 10x Genomics solutions, data | works with: Cell Ranger | Restricted | SCR_018555 | SciCrunch Registry | Loupe Cell Browser 4.0 | 2026-09-19 12:55:18 | 187 | |||||||||
|
Coronavirus Immunotherapy Consortium Resource Report Resource Website 10+ mentions |
Coronavirus Immunotherapy Consortium (RRID:SCR_018258) | CoVIC | consortium, data or information resource, organization portal, portal, topical portal | Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. | COVID-19, antibody, antibody based therapy, coronavirus, SARS-CoV-2, antibody collection, analysis, potency in vitro, efficacy in vivo, standardized assay, identify mAb, therapeutic molecule, vulnerable population protect, database, data |
is related to: La Jolla Institute for Immunology is related to: Duke University; North Carolina; USA is related to: CoVIC-DB Database |
COVID-19 | Free, Freely available | SCR_018258 | SciCrunch Registry | 2026-09-19 12:55:18 | 14 | ||||||||
|
METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | data access protocol, software resource, web service | Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository. | Annotate data, genomics study, microbiome, metadata, genomics, data |
is related to: NCBI Sequence Read Archive (SRA) is related to: NCBI |
NIH | Free, Freely available | SCR_018494 | SciCrunch Registry | METAdata of GEnomics studies on a web based NOTEbook | 2026-09-19 12:55:18 | 1 | ||||||||
|
Stanford University Human Immune Monitoring Center Core Facility Resource Report Resource Website 1+ mentions |
Stanford University Human Immune Monitoring Center Core Facility (RRID:SCR_018266) | HIMC | access service resource, core facility, data or information resource, service resource | Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data. | Immune monitoring serivce, clinical study, translational study, RNA, protein, data, core facility, USEDit, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Stanford University; Stanford; California |
Open | ABRF_399 | https://coremarketplace.org/?FacilityID=399 | SCR_018266 | SciCrunch Registry | Stanford University - Human Immune Monitoring Center, Human Immune Monitoring Center (HIMC) | 2026-09-19 12:55:18 | 1 | ||||||
|
ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, service resource, software resource, web service | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R01 GM061867; NIGMS R35 GM118078 |
PMID:28079879 | Free, Freely available | SCR_018248 | SciCrunch Registry | ClusPro 2.0 | 2026-09-19 12:55:18 | 979 | |||||||
|
Redivis Resource Report Resource Website 10+ mentions |
Redivis (RRID:SCR_023111) | Redivis | data repository, service resource, software repository, software resource, storage service resource | Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data. | Data platform, central hub, discover, access, analyze, data, academic research, hosting datasets, analyzing datasets | is related to: DataCite | Restricted | r3d100014398, 10.57761, SCR_024550 | https://search.datacite.org/repositories/sul.swbvyu, https://doi.org/10.57761/, https://dx.doi.org/10.57761, https://doi.org/10.17616/R31NJNLQ | SCR_023111 | SciCrunch Registry | Red Vis | 2026-09-19 12:55:30 | 14 | ||||||
|
Allen Brain Atlas Tools Resource Report Resource Website |
Allen Brain Atlas Tools (RRID:SCR_023855) | ABAT | software resource | Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas. | Allen Human Brain Atlas, MATLAB functions, Allen Brain Atlas data, data, read, analyze, visualize | is related to: Allen Institute for Brain Science | Free, Freely available | SCR_023855 | SciCrunch Registry | ABAT (Allen Brain Atlas Tools) | 2026-09-19 12:55:39 | 0 | ||||||||
|
EarthCube Resource Report Resource Website 1+ mentions |
EarthCube (RRID:SCR_024576) | data or information resource, portal, topical portal | Platform provides tools, data, services, apps and community resources for geoscience researchers. EarthCube community works together to influence how data will be collected accessed, analyzed, visualized, shared and archived; participate in interdisciplinary and collaborative research; and contribute to transformation of geoscience research through emerging practices of digital scholarship, data and software stewardship, and open science. | open science, geoscience, geoscience interdisciplinary and collaborative research, tools, data, services, apps, community resources, |
is listed by: DataCite has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.25352 | SCR_024576 | SciCrunch Registry | 2026-09-19 12:55:45 | 1 | |||||||||
|
California Coastal Atlas Resource Report Resource Website |
California Coastal Atlas (RRID:SCR_024554) | data or information resource, portal, topical portal | Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes. | California coast, water, climate, coastal processes, data, informing public policy, |
is listed by: DataCite has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.4246 | SCR_024554 | SciCrunch Registry | 2026-09-19 12:55:45 | 0 | |||||||||
|
Cerner Enviza Resource Report Resource Website |
Cerner Enviza (RRID:SCR_024435) | commercial organization | American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases. | Oracle, Cerner, data, analytics, oncology, rare disease, | SCR_024435 | SciCrunch Registry | 2026-09-19 12:55:44 | 0 | ||||||||||||
|
Allen Mouse Brain Reference Atlas Resource Report Resource Website 100+ mentions |
Allen Mouse Brain Reference Atlas (RRID:SCR_002978) | ABA, ARA, ABA Mouse Brain | atlas, data or information resource, reference atlas | Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer. | 3D, map, gene, expression, data, adult, mouse, brain, interactive, image |
is used by: NIF Data Federation is used by: BICCN is related to: BrainStars is related to: PubAnatomy is related to: Integrated Brain Gene Expression is related to: Allen Brain Atlas API is related to: 3DBar is related to: aGEM is related to: CellTax vignette is related to: Blue Brain Cell Atlas is related to: Allen Mouse Brain Common Coordinate Framework is related to: SHARCQ is related to: Enhancer Trap Line Browser is related to: Linked Neuron Data has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas works with: MeshView works with: Brain Gene Expression Analysis toolbox works with: VisuAlign works with: MIRACL |
Free, Freely available | SCR_013286, nlx_21010, nif-0000-00508 | http://mouse.brain-map.org/atlas/index.html, http://mouse.brain-map.org/ | SCR_002978 | SciCrunch Registry | Allen Mouse Brain Reference Atlas, Allen Reference Atlases, ABA Adult Mouse Brain, ARA ontology | 2026-09-19 12:55:52 | 453 | ||||||
|
BioJava Project Resource Report Resource Website 50+ mentions |
BioJava Project (RRID:SCR_007180) | BioJava | data processing software, software application, software resource | Project dedicated to providing Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. Sponsor: BioJava is not formally funded by any grants. Through the OBF they have received sponsorship from Sun Microsystems, Apple Computers and NESCent. The initial development of the phylogenetics module was undertaken as a Google Summer of Code 2007 project in collaboration with NESCent. | biojava, framework, biological, data, analytical, statistical, file, manipulation, 3d structure, application, bioinformatics |
is listed by: Debian is listed by: OMICtools |
OMICS_04848, nif-0000-30181 | https://sources.debian.org/src/libbiojava4-java/ | SCR_007180 | SciCrunch Registry | The BioJava Project, BioJava Project | 2026-09-19 12:55:56 | 85 | |||||||
|
Duke University Medical Center Neuropsychiatric Imaging Research Laboratory Resource Report Resource Website 1+ mentions |
Duke University Medical Center Neuropsychiatric Imaging Research Laboratory (RRID:SCR_007124) | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Neuropsychiatric Imaging Research Laboratory (NIRL) analyze magnetic resonance images to research numerous psychiatric disorders including depression, bipolar disorder, and post traumatic stress disorder. NIRL also develop new methods for MR image processing to improve quality and reliability of research in the field of neuroimaging. The laboratory computer resources include Sun MicroSystems SPARC workstations, Windows PCs, over 3 terabytes of online hard disk space, and a web server system. The lab has a site filtered anonymous ftp server system for data transfer. There are individual offices for visiting fellows and analysts for image processing as well as shared work-study rooms and conference facilities. | allele, antioxidant, apolipoprotein-e, biomedical, bipolar, child, cognitive, data, depression, disorder, geriatric, hard disk, hiv, imaging, impairment, infection, magnetic resonance, magnetic resonance image, marijuana, mri, neurobiology, neurofibromatosis, neurological, neuropsychiatric, neuroscience, post traumatic stress disorder, prognostic, psychiatric, ptsd, research, server, terabyte, vascular, neuroimaging | has parent organization: Duke University; North Carolina; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10212 | http://nirlweb.mc.duke.edu/ | SCR_007124 | SciCrunch Registry | DMC NIRL | 2026-09-19 12:55:56 | 1 | |||||||
|
Human Microbiome Project Resource Report Resource Website 100+ mentions |
Human Microbiome Project (RRID:SCR_012956) | HMP, NIH HMP, HMP1 | data or information resource, portal, project portal | NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016. | generate, resource, human, body, microbiota, analyze, health, disease, metagenomic, DNA, sequesncing, data |
lists: Pathogen Portal lists: DNACLUST lists: QIIME lists: mothur lists: Greengenes lists: Ribosomal Database Project lists: DeconSeq lists: FragGeneScan lists: MetAMOS lists: MetaPhlAn lists: MetaPhyler lists: METAREP lists: PRINSEQ lists: TagCleaner lists: BioCyc lists: MG-RAST lists: Core Gene Evaluation Script lists: IMG System lists: RAST Server lists: GINGKO lists: inVUE lists: LEfSe lists: Metastats lists: MicrobiomeUtilities lists: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP lists: HMPTrees lists: Simrank lists: speciateIT lists: Unifrac lists: Fast-Unifrac lists: SitePainter lists: BMTagger lists: HUMAnN lists: Metapath lists: IMG System is related to: biobakery is related to: Integrative Human Microbiome Project is related to: MicrobiomeDB is related to: Broad Institute Genomics Platform has parent organization: National Institutes of Health is parent organization of: HMP Data Analysis and Coordination Center |
NIH | nif-0000-25316 | https://www.hmpdacc.org/ihmp/, https://www.hmpdacc.org/hmp | http://nihroadmap.nih.gov/hmp/ | SCR_012956 | SciCrunch Registry | Human Microbiome Project, NIH HMP, HMP1, HMP, NIH Human Microbiome Project | 2026-09-19 12:56:01 | 414 | |||||
|
Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | data processing software, software application, software resource | Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows. | trimming, task, paired, end, single, data, next, generation, sequencing, filtering, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill |
BLE/BMELV Verbundprojekt ; BMBF |
PMID:24695404 DOI:10.1093/bioinformatics/btu170 |
biotools:trimmomatic, OMICS_01097 | https://omictools.com/trimmomatic-tool, https://bio.tools/trimmomatic, https://sources.debian.org/src/trimmomatic/ | SCR_011848 | SciCrunch Registry | Trimmomatic v 0.32 | 2026-09-19 12:56:01 | 23444 | |||||
|
SCENIC Resource Report Resource Website 100+ mentions |
SCENIC (RRID:SCR_017247) | data processing software, software application, software resource | Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data. | single, cell, regulatory, network, inference, clustering, simultaneous, gene, reconstruction, single, RNA-seq, data | ERC Consolidator Grant ; Foundation Against Cancer ; Special Research Fund (BOF) KU Leuven ; The Research Foundation - Flanders |
PMID:28991892 | Free, Available for download, Freely available | https://aertslab.org/#scenic | SCR_017247 | SciCrunch Registry | 2026-09-19 12:56:07 | 161 |
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
