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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BioAssay Express Resource Report Resource Website 1+ mentions |
BioAssay Express (RRID:SCR_017594) | data access protocol, service resource, software resource, web service | Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations. | Annotating, bioassay, protocol, semantic, web, term, ontology | is listed by: OMICtools | NCATS R44 TR000185 | DOI:10.7717/peerj-cs.61 | Free, Freely available | https://github.com/cdd/bioassay-template | SCR_017594 | 2026-09-19 12:53:42 | 1 | |||||||
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Data Information System - DAISY Resource Report Resource Website 1+ mentions |
Data Information System - DAISY (RRID:SCR_017472) | DAISY | software resource, web application | Open source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement. | Map, data, flow, GDPR | Free, Available for download, Freely available | https://github.com/elixir-luxembourg/daisy | SCR_017472 | DAta Information SYstem | 2026-09-19 12:53:41 | 2 | ||||||||
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Biotite Resource Report Resource Website 1+ mentions |
Biotite (RRID:SCR_017593) | data analysis software, data processing software, data visualization software, service resource, software application, software resource, software toolkit | Software Python package bundling popular tasks in computational molecular biology, from sequence analysis to structural bioinformatics. Comprehensive library for computational molecular biology. Package features sequence and structure data analysis and editing functionality, support for common sequence and structure file formats, visualization capabilities, interfaces to external software (MSA software, BLAST, DSSP). Operating system(s): Windows, OS X, Linux. | works with: Entrez | DOI:10.1186/s12859-018-2367-z | Free, Available for download, Freely available | SCR_017593 | 2026-09-19 12:53:42 | 5 | ||||||||||
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Transcriptomics Explorer Resource Report Resource Website 100+ mentions |
Transcriptomics Explorer (RRID:SCR_017567) | data analysis software, data processing software, data visualization software, service resource, software application, software resource | Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus. | Visualize, analyze, transcriptomic, data, cell, type, mouse, human, Allen, database, multiple, cortical, area, cortex, hippocampus | works with: Allen Brain Atlas | Free, Freely available | https://celltypes.brain-map.org/rnaseq/human/cortex, https://celltypes.brain-map.org/rnaseq/mouse/cortex-and-hippocampus, | SCR_017567 | 2026-09-19 12:53:42 | 108 | |||||||||
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Willoughby–Hoye Python Scripts A-D Resource Report Resource Website 1+ mentions Issue |
Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) | data analysis software, data processing software, software application, software resource | Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889. | Python, NMR, script, caluclating, chemical, shift, data | NIA R01 AG039468 | PMID:24556787 PMID:31591889 |
Free, Freely available | SCR_017562 | 2026-09-19 12:53:42 | 1 | |||||||||
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swMath Resource Report Resource Website 1+ mentions |
swMath (RRID:SCR_017607) | data or information resource, database, software repository, software resource | Repository of math software. Information service for mathematical software. Provides access to database of information on mathematical software and includes systematic linking of software packages with relevant mathematical publications. Database for references on mathematical software. | Repository, math, infromation, service, publication, database | Leibniz Association | Free, Freely available | r3d100014573 | https://doi.org/10.17616/R31NJNQL | SCR_017607 | 2026-09-19 12:53:43 | 2 | ||||||||
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shinyGEO Resource Report Resource Website |
shinyGEO (RRID:SCR_017605) | analysis service resource, production service resource, service resource, software resource, web application | Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. | Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools |
uses: Shiny is listed by: Debian is listed by: bio.tools has parent organization: Eastern Connecticut State University; Connecticut; United States works with: Gene Expression Omnibus (GEO) |
Google Summer of Code | PMID:27503226 | Free, Available for download, Freely available | biotools:shinygeo | https://gdancik.github.io/shinyGEO/, https://bio.tools/shinygeo | SCR_017605 | 2026-09-19 12:53:43 | 0 | ||||||
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GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | analysis service resource, atlas, data analysis service, data or information resource, database, production service resource, service resource | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | Gene ATLAS, Gene Atlas | 2026-09-19 12:53:42 | 158 | |||||||||
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SciGraph Resource Report Resource Website 1+ mentions |
SciGraph (RRID:SCR_017576) | data processing software, data visualization software, software application, software resource, standalone software | Software tool to represent ontologies and data described using ontologies as Neo4j graph. Ontology serving middleware tool using Neo4J as base server, able to ingest ttl files, and serve them to quickly create services that can underpin autocomplete, term lookup and tree traversal. | Ontology, data, Neo4j graph, server, ttl, file |
is used by: SPARC Portal is used by: SciCrunch is used by: CINERGI is used by: Human Brain Project |
Free, Available for download, Freely available | SCR_017576 | 2026-09-19 12:53:42 | 3 | ||||||||||
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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 | MySampleSize | 2026-09-19 12:53:43 | 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 | reference genome manager | 2026-09-19 12:53:42 | 7 | ||||||
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PoloPlus USB Drive software Resource Report Resource Website 10+ mentions |
PoloPlus USB Drive software (RRID:SCR_017614) | data analysis software, data processing software, software application, software resource | Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB. | LeOra Software LLC, grouped, data, analysis, USB, drive, probit, logit | Restricted | SCR_017614 | Probit Or LOgit Plus USB Drive, PoloPlus USB Drive | 2026-09-19 12:53:43 | 35 | ||||||||||
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StatPackets Resource Report Resource Website |
StatPackets (RRID:SCR_017613) | data or information resource, narrative resource, standard specification | Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together. | Standardized, method, export, statistical, data, KOMP, result, analysis, together | is related to: Knockout Mouse Project | Free, Freely available | SCR_017613 | 2026-09-19 12:53:43 | 0 | ||||||||||
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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 | 2026-09-19 12:53:41 | 0 | |||||||||
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EBRAINS Knowledge Graph Resource Report Resource Website 1+ mentions |
EBRAINS Knowledge Graph (RRID:SCR_017612) | data management software, data or information resource, database, service resource, software application, software resource | Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems. | Metadata, managing, system, neuroscience, experimental, data, human, brain, graph, database, terminology, ontology |
is related to: Human Brain Project is related to: MarmotGraph |
European Union’s Horizon 2020 Framework Programme for Research and Innovation 720270; European Union’s Horizon 2020 Framework Programme for Research and Innovation 785907 |
Free, Freely available | https://kg.humanbrainproject.eu/ | SCR_017612 | New Enabling Infrastructure for Neuroscience Knowledge Graph, EBRAINS Knowledge Graph (KG), HBP Knowledge Graph | 2026-09-19 12:53:43 | 8 | |||||||
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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 | 2026-09-19 12:53:42 | 0 | ||||||||
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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 | RJAGS library | 2026-09-19 12:53:42 | 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 | project-dare, Delivering Agile Research Excellence on European e-Infrastructures | 2026-09-19 12:53:41 | 1 | |||||||||
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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 | 2026-09-19 12:53:41 | 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 | pyDynamo, python Dynamo | 2026-09-19 12:53:41 | 2 |
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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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