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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
geocoding Resource Report Resource Website 10+ mentions |
geocoding (RRID:SCR_016007) | data analysis software, data analytics software, data processing software, software application, software resource | Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude. | software, data, analysis, geo-location, residential, environment, abcd, study |
has parent organization: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016007 | ABCD geocoding, ABCD geocoding project, geocoding project | 2026-09-05 06:28:02 | 23 | ||||||||
|
Stimfit Resource Report Resource Website 10+ mentions |
Stimfit (RRID:SCR_016050) | data analysis software, data processing software, software application, software resource | Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. | electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysis |
uses: NumPy uses: SciPy |
European Research Council ; Gatsby Charitable Foundation ; Wellcome Trust |
PMID:24600389 | Free, Available for download | SCR_016050 | 2026-09-05 06:28:03 | 41 | ||||||||
|
Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML, https://sources.debian.org/src/clonalframe/ | SCR_016060 | ClonalFrameML | 2026-09-05 06:28:03 | 407 | |||||
|
DEAP - Data Exploration and Analysis Portal Resource Report Resource Website 10+ mentions |
DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) | DEAP | data access protocol, software resource, web service | Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States. | data, exploration, analysis, portal, brain, development, child, health, United, States, long, term, study | is related to: ABCD Study | Free, Available for download | SCR_016158 | DEAP: Data Exploration and Analysis Portal | 2026-09-05 06:28:04 | 18 | ||||||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NIGMS R01 ; NIH R01 AI47745; NIH U01 AI43638; NSF DBI-0096033; NSF DEB-9996118; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/, https://veg.github.io/hyphy-site/, https://github.com/veg/hyphy, https://bio.tools/HyPhy, | SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-09-05 06:28:04 | 1586 | |||||
|
Gubbins Resource Report Resource Website 500+ mentions |
Gubbins (RRID:SCR_016131) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 098051 | PMID:25414349 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_14386 | https://sources.debian.org/src/gubbins/ | SCR_016131 | Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences | 2026-09-05 06:28:04 | 604 | |||||
|
Mass Univariate ERP Toolbox Resource Report Resource Website 1+ mentions |
Mass Univariate ERP Toolbox (RRID:SCR_016108) | data analysis software, data processing software, data visualization software, software application, software resource | Software toolkit of Matlab functions for analyzing and visualizing large numbers of t-tests performed on event-related potential data. The toolbox supports within-subject and between-subject t-tests with false discovery rate controls and control of the family-wise error rate via permutation tests. | matlab, analysis, t test, statistic, erp, event related potential, visualization, neuroimaging, erf, magnetic, resonance, imaging | requires: MATLAB | NIA AG08313; NICHD HD22614 |
PMID:21895683 | Free, Available for download | https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox | SCR_016108 | 2026-09-05 06:28:03 | 6 | |||||||
|
Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | data analysis software, data processing software, software application, software resource | Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis. | dwi, t1, tractography, algorithm, white matter, bundle, gray matter, shape, analysis, network, workflow | CPRIT RR150054; NIMH MH086633; NIMH MH092335; NSF DMS-1407655; NSF DMS1127914; NSF SES-1357666 |
Free for non-commercial use, Available for download | SCR_016232 | 2026-09-05 06:28:05 | 0 | ||||||||||
|
OpenEx Resource Report Resource Website 100+ mentions |
OpenEx (RRID:SCR_016230) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit that is designed for configuration and control of TDT hardware. It can also display and analyze neurophysiology data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tdt, analysis, neurophysiology, hardware, companion software, control, configuration, neuroimaging, eeg, stimulation | has parent organization: Tucker-Davis Technologies | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016230 | The OpenEx Software Suite, OpenEx suite | 2026-09-05 06:28:05 | 103 | |||||||||
|
Gff2aplot Resource Report Resource Website |
Gff2aplot (RRID:SCR_016128) | data processing software, data visualization software, software application, software resource | Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis. | alignment, pair-wise, plot, genomic, sequence, visualize, together, annotate, analysis, parameter, dataset, |
is listed by: Debian is listed by: OMICtools |
PMID:14668236 | Free, Available for download | OMICS_19949 | https://sources.debian.org/src/gff2aplot/ | SCR_016128 | 2026-09-05 06:28:04 | 0 | |||||||
|
nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | Human Frontiers Science Program RGY0088; NSF CBET-1351692; NSF IOS-1550994 |
Free, Available for download, Freely available | SCR_016209 | Nelpy (Neuroelectrophysiology) | 2026-09-05 06:28:05 | 3 | ||||||||
|
UTHSCSA ImageTool Resource Report Resource Website 100+ mentions |
UTHSCSA ImageTool (RRID:SCR_016208) | IT | data processing software, image analysis software, image processing software, software application, software resource | Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images. | image, analysis, processing, data, acquisition, compression, modification | has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA | Free, Available for download, Runs on Windows | http://en.bio-soft.net/draw/ImageTool.html | SCR_016208 | UTHSCSA Image Tool, UTHSCSA ImageTool (IT) | 2026-09-05 06:28:05 | 120 | |||||||
|
CATNAP Resource Report Resource Website 10+ mentions |
CATNAP (RRID:SCR_016170) | data analysis software, data processing software, software application, software resource | Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, analysis, | PMID:26044712 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016170 | CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels | 2026-09-05 06:28:04 | 49 | |||||||||
|
GoldWave Resource Report Resource Website 50+ mentions |
GoldWave (RRID:SCR_016189) | data analysis software, data processing software, software application, software resource | Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes. | audio, sound, analysis, acquisition, visualization, record, edit, analysis, auditory | Commercially available, Available for purchase | SCR_016189 | 2026-09-05 06:28:05 | 88 | |||||||||||
|
GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | data access protocol, data or information resource, database, software resource, web service | Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis. | database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformatics |
is listed by: OMICtools is related to: University of British Columbia; British Columbia; Canada |
Canadian Foundation for Innovation infrastructure ; CIHR ; NIH MH111099; NSERC Discovery Grant |
DOI:10.1101/320861 | Free, Available for download, Freely available | https://github.com/PavlidisLab/gotrack, https://omictools.com/gotrack-tool | SCR_016399 | 2026-09-05 06:28:08 | 1 | |||||||
|
RELION Resource Report Resource Website 100+ mentions |
RELION (RRID:SCR_016274) | data analysis software, data processing software, software application, software resource, standalone software | Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy. | cryo, cryogenic, cryo em, determination, analysis, bayesian, statistic, map, maximum a posteriori, electron, cryomicroscopy |
is listed by: Debian is listed by: OMICtools |
UK Medical Research Council | PMID:23000701 | Free, Available for download, Tutorial available | OMICS_15597 | https://sources.debian.org/src/relion-bin+mpi+gui/ | SCR_016274 | RELION, REgularised LIkelihood OptimisatioN, RELION-3 | 2026-09-05 06:28:06 | 440 | |||||
|
Vensim Resource Report Resource Website 10+ mentions |
Vensim (RRID:SCR_016394) | simulation software, software application, software resource | Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models. | performance, system, Ventana Systems Inc, model, modelling, analysis | Commercially available, Available for purchase | SCR_016394 | 2026-09-05 06:28:08 | 14 | |||||||||||
|
OmicsBean Resource Report Resource Website 100+ mentions |
OmicsBean (RRID:SCR_016322) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users. | GeneForHealth Biotech Inc (GFK), data, analysis, genome, proteome, metabolome, network, molecular, mechanism, model, collect, store, analytic, multi, omic | Commercially available, Demo available | SCR_016322 | 2026-09-05 06:28:06 | 189 | |||||||||||
|
ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data. | bacterial, archaeal, RNA, sequencing, data, analysis, genome, annotation, statistic, visualization, protein, interaction, prediction, grouping, go, ontology, gene, differential, circular |
is related to: Infernal is related to: Vienna RNA is related to: Biopython is related to: MEME Suite - Motif-based sequence analysis tools is related to: Segemehl |
Free, Freely available, Available for download | SCR_016326 | 2026-09-05 06:28:07 | 10 | ||||||||||
|
MxPro QPCR Resource Report Resource Website 500+ mentions |
MxPro QPCR (RRID:SCR_016375) | data analysis software, data processing software, software application, software resource | Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pcr, qpcr, polymerase, qualitative, analysis, nucleic, acid, gene | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016375 | MxPro QPCR Software | 2026-09-05 06:28:07 | 543 |
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
