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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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Orientation Distribution Function in Constant Solid Angle (CSA-ODF) Resource Report Resource Website |
Orientation Distribution Function in Constant Solid Angle (CSA-ODF) (RRID:SCR_014158) | CSA ODF | data processing software, data visualization software, software application, software resource, software toolkit | A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI. | matlab, toolbox, imaging orientation, diffusion weighted mri, image reconstruction, modeling |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
Available to the research community | SCR_014158 | SciCrunch Registry | Orientation Distribution Function in Constant Solid Angle | 2026-10-24 12:47:15 | 0 | ||||||||
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AcqKnowledge Software Resource Report Resource Website 100+ mentions |
AcqKnowledge Software (RRID:SCR_014279) | data acquisition software, data analysis software, data processing software, simulation software, software application, software resource | A software program that allows the user to perform data acquistion, stimulation and analyses. Users do not need to know the programming language or a new protocol view. AcqKnowledge Software is compatible with MP150 Research Systems, MP36R Research Systems, and MRI and fMRI Setups. A variety of offline and online analysis tools allows users to customize data recordings and targeted analyses. The software can perform automated analysis routines, output a range of stimulus paradigms, and allows users to record from multiple hardware devices simultaneously. | data acquisition software, simulation software, data analysis software, record data, target analysis, automation, stimulus paradigm | has parent organization: Biopac Systems Inc | SCR_014279 | SciCrunch Registry | 2026-10-24 12:47:15 | 257 | |||||||||||
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NiiStat Resource Report Resource Website 50+ mentions |
NiiStat (RRID:SCR_014152) | data analysis software, data processing software, software application, software resource, source code | A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data. | matlab script, source code, data analysis, neuroimaging data, clinical population |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Medical University of South Carolina; South Carolina; USA |
Available to the research community | http://www.nitrc.org/plugins/mwiki/index.php/niistat:MainPage | SCR_014152 | SciCrunch Registry | 2026-10-24 12:47:15 | 88 | |||||||||
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MassLynx Resource Report Resource Website 5000+ mentions |
MassLynx (RRID:SCR_014271) | data acquisition software, data analysis software, data management software, data processing software, software application, software resource | Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data acquisition software, data analysis software, data management software, mass spectrometry | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014271 | SciCrunch Registry | MassLynx MS Software | 2026-10-24 12:47:14 | 5809 | |||||||||
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Ruby NIfTI Resource Report Resource Website |
Ruby NIfTI (RRID:SCR_014164) | software library, software resource, software toolkit | A library for handling NIfTI data in the Ruby programming language. Ruby NIfTI supports basic read and write access to NIfTI files, including basic and extended header information and image information. It doesn't attempt to touch the image data but it does provide access to qform and sform orientation matrices. It also provides a nice interface to get at NIfTI info from within Ruby. | nifti library, ruby, nifti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard University; Cambridge; United States |
https://github.com/brainmap/nifti | SCR_014164 | SciCrunch Registry | 2026-10-24 12:47:13 | 0 | ||||||||||
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SCORE Resource Report Resource Website 100+ mentions |
SCORE (RRID:SCR_014165) | data or information resource, experimental protocol, narrative resource | A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard. | experiment protocol, method, different image algorithm, quantitative score |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NLM HHSN276201000584P; NIBIB 1R41 EB011796 |
SCR_014165 | SciCrunch Registry | 2026-10-24 12:47:15 | 481 | ||||||||||
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Quantity One 1-D Analysis Software Resource Report Resource Website 10000+ mentions |
Quantity One 1-D Analysis Software (RRID:SCR_014280) | data acquisition software, data analysis software, data processing software, software application, software resource | Software used for Bio-Rad imaging systems to acquire, quantitate, and analyze a variety of data. The software allows automatic configuration of imaging systems with appropriate filters, lasers, LEDs, and other illumination sources. It also contains tools for automated analysis of tests and assays such as 1-D electrophoretic gels, western blots, and colony counts. | data analysis software, data acquisition software, automatic configuration, imaging system, automated analysis | SCR_016622 | SCR_014280 | SciCrunch Registry | 2026-10-24 12:47:15 | 13127 | |||||||||||
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Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data Resource Report Resource Website |
Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data (RRID:SCR_014163) | data analysis software, data processing software, image analysis software, software application, software resource | An implementation of standard PCA algorithms for use on scalar or vector data sets. Kernel PCA is implemented in this class, where the data sets are scalar or vector valued functions assigned at each of the points in a PointSet. A Gaussian Distance Kernel class is provided with the PCA class. | pca algorithm, shape analysis, data analysis software, scalar data set, vector data set |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
Available to the research community | SCR_014163 | SciCrunch Registry | 2026-10-24 12:47:13 | 0 | ||||||||||
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StepOne Software Resource Report Resource Website 100+ mentions |
StepOne Software (RRID:SCR_014281) | data analysis software, data processing software, software application, software resource | A software program for the Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems. StepOne software allows the user to open and analyze experiments generated from either the StepOne or the StepOnePlus system. Users can set up experiments, send experiments to the instrument, control the instrument settings, and collect and analyze data. | applied biosystems step one, pcr, data analysis software, instrument management software, experimental control | Pay for product | https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/StepOne-and-StepOnePlus-Real-Time-PCR-System.html | SCR_014281 | SciCrunch Registry | 2026-10-24 12:47:15 | 269 | ||||||||||
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PsyGeNET Resource Report Resource Website 10+ mentions |
PsyGeNET (RRID:SCR_014406) | data analysis software, data or information resource, data processing software, database, software application, software resource | Knowledge platform on psychiatric disorders and their genes. Resource for exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of database and set of analysis tools and is the result of the integration of information from DisGeNET and data extracted from the literature by text mining, followed by curation by domain experts. | psychiatric disease, associated gene, database, analysis tool, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools |
Psychiatric disorder | DOI:10.1093/bioinformatics/btv301 | Available for the research community | biotools:psygenet2r | https://bio.tools/psygenet2r | SCR_014406 | SciCrunch Registry | Psychiatric disorders Gene association NETwork, Psychiatric disorders Gene association Network | 2026-10-24 12:47:16 | 11 | |||||
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Lifestyle Interventions for Expectant Moms (LIFE-Moms) Resource Report Resource Website |
Lifestyle Interventions for Expectant Moms (LIFE-Moms) (RRID:SCR_014376) | LIFE-Moms | data or information resource, organization portal, portal, resource | A consortium whose overall goal is to identify effective behavioral and lifestyle interventions that will improve weight, glycemic control and other pregnancy-related outcomes in obese and overweight pregnant women, and determine whether these interventions reduce obesity and metabolic abnormalities in their children. The study/consortium is comprised of seven clinical centers, with each clinical center conducting its own trial. Additional information on the consortium and individual trials is located in the Consortium Summaries tab. | pregnant, pregnancy, obesity, metabolic abnormality, behavioral intervention, lifestyle intervention, clinical trial |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources |
Obesity | NIDDK ; NHLBI ; NICHD ; National Center for Complementary and Integrative Health ; Office of Research on Womens Health ; Office of Behavioral and Social Sciences Research |
Synopses available, Users may access trial data at clinicaltrial.gov | http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx | SCR_014376 | SciCrunch Registry | Lifestyle Interventions for Expectant Moms | 2026-10-24 12:47:16 | 0 | |||||
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Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) Resource Report Resource Website |
Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) (RRID:SCR_014378) | LURN | resource | A research consortium with the long term goal of developing and testing measurement tools to describe symptoms of lower urinary tract dysfunction (LUTD) in women and men. The group plans to study targeted populations of patients with LUTD in order to expand our understanding of the causes of symptoms and common ways that symptoms change over time. The researchers will also collect biosamples from patients for current and future study of LUTD. | lower urinary tract, dysfunction, research, consortium, lutd, symptom, biosample |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology |
NIDDK 1U01DK097776 | SCR_014378 | SciCrunch Registry | Symptoms of Lower Urinary Tract Dysfunction Research Network | 2026-10-24 12:47:16 | 0 | ||||||||
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Muse: Portable Scalp EEG Device (Muse S Athena) Resource Report Resource Website 100+ mentions |
Muse: Portable Scalp EEG Device (Muse S Athena) (RRID:SCR_014418) | instrument resource, mobile app, software application, software resource | It is a portable scalp electroencephalography (EEG) system that can be used to measure brain activity. It is battery powered and has four active electrodes located at 10-20 coordinates TP9, AF7, AF8, and TP10, a common mode reference, and a driven right leg. It includes an accelerometer and gyroscope, and works with desktop and mobile EEG acquisition and visualization software. Muse 2 expands upon the first model with increasingly robust hardware. | portable, scalp electroencephalography, brain activity, mobile app, data acquisition software, data analysis software | Ontario Centres of Excellence ; Natural Sciences and Engineering Research Council of Canada |
DOI:10.1371/journal.pone.0130129 | Public, Commercial product, Headband requires purchase, App is free | SCR_014418 | SciCrunch Registry | , Muse 2, Muse: the brain sensing headband | 2026-10-24 12:47:16 | 326 | ||||||||
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FlexField Software Resource Report Resource Website 1+ mentions |
FlexField Software (RRID:SCR_014420) | software application, software resource, standalone software, systems interoperability software | Transformation software designed to help model and change Oracle account charts. This can be used to reorganize Oracle accounts due to events such as mergers, acquisitions, regulatory requirements and the need for more ranges when the data outgrows the range of the current chart of accounts. FlexField transforms an existing accounting flexfield segment structure, values, code combinations, and CCIDs according to user mappings, and applies the new code combinations and CCIDs. It propagates the change throughout an existing E-Business Suite data, everywhere the accounting flexfield is used. It removes the old code combinations and CCIDs, and aligns the new Chart of Accounts (COA) so that all balances belonging to a single CCID are summarized into a single line. | software, oracle, ccid, account chart, segment structure, accounting, chart of accounts | Commercial product, License fee | SCR_014420 | SciCrunch Registry | 2026-10-24 12:47:16 | 2 | |||||||||||
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Clinical Islet Transplantation Consortium (CITC) Resource Report Resource Website 1+ mentions |
Clinical Islet Transplantation Consortium (CITC) (RRID:SCR_014385) | CITC, CIT | access service resource, service resource | Network of clinical centers and a data coordinating center established to conduct studies of islet transplantation in patients with type 1 diabetes. | type 1 diabetes, consortium, network, islet transplantation, clinical |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is listed by: Diabetes Research Centers |
Type 1 diabetes, Diabetes | NIAID ; NIDDK U01 DK070431 |
SCR_014385 | SciCrunch Registry | Clinical Islet Transplantation Consortium | 2026-10-24 12:47:16 | 1 | |||||||
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Navios Software Resource Report Resource Website 1+ mentions |
Navios Software (RRID:SCR_014421) | data acquisition software, data analysis software, data processing software, software application, software resource | Used in tandem with the Navios Flow Cytometer in order to acquire data for use in analyzing cellular characteristics. | flow cytometry, machine software, control software, data analysis software, data acquisition software, lymphocyte, multicolor | Commercial product | http://www.beckman.com/coulter-flow-cytometry/instruments/flow-cytometers/navios | SCR_014421 | SciCrunch Registry | Navios Tetra Software | 2026-10-24 12:47:18 | 3 | |||||||||
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BD Accuri C6 Plus Resource Report Resource Website 50+ mentions |
BD Accuri C6 Plus (RRID:SCR_014422) | data acquisition software, data analysis software, data processing software, software application, software resource | Software used for collecting and analyzing flow cytometry data. Files can be exported in FCS 3.1 format for import into other flow cytometry analysis programs such as FCS Express™ software and FlowJo™ software. | data analysis software, data acquisition software, flow cytometry, flow cytometry analysis program | Commercial product | SCR_014422 | SciCrunch Registry | 2026-10-24 12:47:16 | 56 | |||||||||||
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Restoring Insulin Secretion Consortium (RISE) Resource Report Resource Website |
Restoring Insulin Secretion Consortium (RISE) (RRID:SCR_014383) | RISE | consortium, data or information resource, database, organization portal, portal | Consortium which includes 3 studies, each assessing the hypothesis that aggressive glucose lowering will lead to recovery of beta-cell function that will be sustained after treatment in those with prediabetes and early type 2 diabetes. | prediabetes, type 2 diabetes, consortium, aggressive glucose lowering, beta cell function, Diabetes |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is listed by: Diabetes Research Centers is listed by: NIDDK Central Repository |
NIDDK | SCR_014383 | SciCrunch Registry | Restoring Insulin Secretion Consortium | 2026-10-24 12:47:16 | 0 | ||||||||
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MSstats Resource Report Resource Website 100+ mentions |
MSstats (RRID:SCR_014353) | data analysis software, data processing software, software application, software resource | A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations. | data independent acquisition, statistical relative quantification, protein, peptide, data analysis software, data processing, data visualization, proteomics |
uses: R Project for Statistical Computing is used by: Skyline is listed by: Bioconductor |
National Science Foundation CAREER award 1054826 | DOI:10.1186/1471-2105-13-S16-S6 | Acknowledgement requested, Available for download | http://www.bioconductor.org/packages/release/bioc/html/MSstats.html | SCR_014353 | SciCrunch Registry | MSStats | 2026-10-24 12:47:18 | 239 | ||||||
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SimThyr Resource Report Resource Website 10+ mentions |
SimThyr (RRID:SCR_014351) | simulation software, software application, software resource | Open source simulation software for thyroid homeostasis, based on published nonlinear model of pituitary thyroid feedback control. Simulates pituitary thyroid feedback control, which allows users to study relationship between structure and behaviour of thyroid homeostasis. | thyroid, homeostasis, simulation, software, modelling, pituitary, model |
is related to: SimulaBeta has parent organization: Ludwig-Maximilians-University; Munich; Germany has parent organization: Ruhr University Bochum; North Rhine-Westphalia; Germany |
PMID:23365787 DOI:10.1080/01969720490443354 DOI:10.1155/2012/351864 DOI:10.5281/zenodo.1303822 |
Free, Available for download, Freely available | DOI:10.5281/zenodo.1303822 | https://doi.org/10.5281/zenodo.1303822 | SCR_014351 | SciCrunch Registry | 2026-10-24 12:47:15 | 11 |
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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.
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