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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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mysamplesize Resource Report Resource Website 1+ mentions |
mysamplesize (RRID:SCR_017575) | data analysis software, data or information resource, data processing software, data visualization software, portal, service resource, software application, software resource | Software tool for experimental design, sample size determination and analysis by Tempest Technologies. | Experimental, design, sample, size, determination, analysis, Tempest Technologies |
is affiliated with: University of California at San Diego; California; USA is affiliated with: University of California at Davis; California; USA |
Restricted | SCR_017575 | SciCrunch Registry | MySampleSize | 2026-09-26 02:16:00 | 1 | |||||||||
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refgenie Resource Report Resource Website 1+ mentions |
refgenie (RRID:SCR_017574) | data management software, service resource, software application, software resource | Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis. | Organize, retrive, share, genome, analysis, reference, assembly, asset, manager, sequence, annotation, file, command, line, interface, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/698704 | Free, Available for download, Freely available | biotools:Refgenie | https://bio.tools/Refgenie | SCR_017574 | SciCrunch Registry | reference genome manager | 2026-09-26 02:16:00 | 7 | ||||||
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TReNA Resource Report Resource Website |
TReNA (RRID:SCR_017458) | data analysis software, data processing software, network analysis software, software application, software resource | Methods for reconstructing transcriptional regulatory networks. | Reconstructing, transcriptional, regulatory, network, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH114788 | Free, Available for download, Freely available | SCR_017458 | SciCrunch Registry | 2026-09-26 02:15:59 | 0 | |||||||||
|
immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | data or information resource, service resource, software application, software resource, text-mining software | Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. | Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract |
is listed by: NIDDK Information Network (dkNET) is listed by: OMICtools |
NIAID ; NIH ; Rappaport Family Institute for Research in the Medical Sciences |
PMID:29912209 | Free, Freely available | SCR_017578 | SciCrunch Registry | 2026-09-26 02:16:00 | 0 | ||||||||
|
rjags Resource Report Resource Website 10+ mentions |
rjags (RRID:SCR_017573) | data analysis software, data processing software, software application, software resource | Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. | Analysis, Bayesian, hierarchical, model, Markov Chain Monte Carlo, simulation |
is listed by: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | https://github.com/cran/rjags/blob/master/INSTALL | SCR_017573 | SciCrunch Registry | RJAGS library | 2026-09-26 02:16:03 | 23 | ||||||||
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Project DARE Resource Report Resource Website 1+ mentions |
Project DARE (RRID:SCR_017538) | DARE | consortium, data or information resource, organization portal, portal, project portal | EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously. | European Union, infrastructure, workflow, connectivity, layer, methodology, integrated, data, Agile | European Union | SCR_017538 | SciCrunch Registry | project-dare, Delivering Agile Research Excellence on European e-Infrastructures | 2026-09-26 02:15:59 | 1 | |||||||||
|
Leica: CM1520 Cryostat Resource Report Resource Website 1+ mentions |
Leica: CM1520 Cryostat (RRID:SCR_017543) | instrument resource | Cryostat for routine histology and cryosectioning including critical applications such as Mohs surgery. Brain sectioning. Actively cooled quick freezing shelf with defrost function and refrigeration system are provided. | Leica, cryostat, histology, surgery, brain, sectioning | This product has been discontinued | https://www.leicabiosystems.com/sites/default/files/media_product-download/2022-01/Leica_CM1520_IFU_2v4O_en.pdf | SCR_017543 | SciCrunch Registry | 2026-09-26 02:15:59 | 4 | ||||||||||
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Dynamo Resource Report Resource Website 1+ mentions |
Dynamo (RRID:SCR_017541) | 3d visualization software, data analysis software, data processing software, data visualization software, image analysis software, image reconstruction software, software application, software resource, time-series analysis software | Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics. | Neuron, dynamic, morphometrics, timelapse, reconstruction, analysis, image | CIHR | Free, Available for download, Freely available | https://padster.github.io/pyDynamo/ | SCR_017541 | SciCrunch Registry | pyDynamo, python Dynamo | 2026-09-26 02:16:03 | 2 | ||||||||
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Worm Lab Resource Report Resource Website 1+ mentions |
Worm Lab (RRID:SCR_017669) | data analysis software, data processing software, software application, software resource | Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays. | MBF Bioscience, imaging, tracking, analysis, C.elegans, nematode, collect, data, worm, omega, bend, coiling, reversal, entanglement, locomotry, behavior, crawling, swimming, assay | Restricted | SCR_017669 | SciCrunch Registry | 2026-09-26 02:16:01 | 8 | |||||||||||
|
Single Cell Developmental Database Resource Report Resource Website 1+ mentions |
Single Cell Developmental Database (RRID:SCR_017546) | SCDevDB | data or information resource, data repository, data set, database, service resource, storage service resource | Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes. | Single, cell, gene, expression, profile, human, development, process, data | GRF Research Project ; RGC General Research Fund |
DOI:10.3389/fgene.2019.00903 | Free, Available for download, Freely available | SCR_017546 | SciCrunch Registry | Single-Cell Developmental Database | 2026-09-26 02:15:59 | 2 | |||||||
|
Transcriptive Resource Report Resource Website |
Transcriptive (RRID:SCR_017545) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. | Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control | Free, Available for download, Freely available | SCR_017545 | SciCrunch Registry | 2026-09-26 02:15:59 | 0 | |||||||||||
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Vesselucida Explorer Resource Report Resource Website 1+ mentions |
Vesselucida Explorer (RRID:SCR_017674) | data analysis software, data processing software, software application, software resource | Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more. | MBF Bioscience, analysis, vasculature, specific, metric, segment, node, count, frequency, anastomoses, vessel, surface, volume | works with: Vesselucida 360 | Restricted | SCR_017674 | SciCrunch Registry | 2026-09-26 02:16:01 | 2 | ||||||||||
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cytoHubba Resource Report Resource Website 100+ mentions |
cytoHubba (RRID:SCR_017677) | data analysis software, data processing software, network analysis software, software application, software resource | Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above. | Identify, network, subnetwork, topological, algorithm, analyze, protein, interaction, hub, object, intercome | is a plug in for: Cytoscape | Ministry of Science and Technology (MOST) ; Taiwan |
PMID:25521941 | Free, Available for download, Freely available | http://hub.iis.sinica.edu.tw/cytoHubba/ | SCR_017677 | SciCrunch Registry | cytoHubba 1.6 | 2026-09-26 02:16:01 | 451 | ||||||
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Cardiff Study of all Wales and North West of England Twins Resource Report Resource Website |
Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) | CaStANET | data or information resource | Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people. | Twins, family, genetic, environmental, origin, trait, collected, behavioral, psychopathological, data | PMID:17539361 | SCR_017480 | SciCrunch Registry | 2026-09-26 02:16:02 | 0 | ||||||||||
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DIANA-mirExTra Resource Report Resource Website 1+ mentions |
DIANA-mirExTra (RRID:SCR_017498) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Software tool for analysis of expression data for microRNA function. | Analysis, expression, data, microRNA, function, DIANA tool | is provided by: DIANA Tools | Free, Freely available | http://diana.imis.athena-innovation.gr/DianaTools/ | SCR_017498 | SciCrunch Registry | Mirextra 2.0 | 2026-09-26 02:15:59 | 1 | ||||||||
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Epigenie Resource Report Resource Website |
Epigenie (RRID:SCR_017494) | data or information resource, portal, topical portal | Collection of epigenetic data browsers and repositories. Repository of epigenetics tools and databases by EpiGenie team. | Repository, epigenetic, tool, database, EpiGenie, data | Free, Available for download, Freely available | SCR_017494 | SciCrunch Registry | 2026-09-26 02:15:59 | 0 | |||||||||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | analysis service resource, data or information resource, portal, production service resource, service resource, software resource | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Maryland School of Medicine; Maryland; USA |
Hearing Health Foundation (Hearing Restoration Project) ; NIDCD R01 DC013817; NIMH MH114788; NIMH R24 MH114815 |
Restricted | SCR_017467 | SciCrunch Registry | gene Expression Analysis Resource | 2026-09-26 02:15:59 | 91 | |||||||
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3D DART Resource Report Resource Website 1+ mentions |
3D DART (RRID:SCR_017588) | service resource, software resource, web application | DNA structure modelling server. Web server for generating custom 3D structural models of DNA with control over local and global conformation. | Generating, custom, 3D, structural, model, DNA, conformation | EU ; Netherlands Organization for Scientific Research |
PMID:19417072 | Free, Freely available | SCR_017588 | SciCrunch Registry | 3DNA-Driven DNA Analysis and Rebuilding Tool | 2026-09-26 02:16:03 | 1 | ||||||||
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cytoNet Resource Report Resource Website |
cytoNet (RRID:SCR_017465) | analysis service resource, data processing software, image analysis software, production service resource, service resource, software application, software resource | Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory. | Cell, population, microscopy, image, network, analysis, quantify, structure, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Free, Freely available | SCR_017465 | SciCrunch Registry | 2026-09-26 02:16:02 | 0 | |||||||||
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IMOTIONS: SMI RED500 Eye Tracker Resource Report Resource Website 1+ mentions |
IMOTIONS: SMI RED500 Eye Tracker (RRID:SCR_017586) | instrument resource | Screen based eye tracker that combines high-speed capabilities at 500 Hz. | Eye, tracker, screen, high, speed, capability, 500Hz | Restricted | SCR_017586 | SciCrunch Registry | 2026-09-26 02:16:00 | 1 |
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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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