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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Optogenetics Resource Center Resource Report Resource Website 1+ mentions |
Optogenetics Resource Center (RRID:SCR_017513) | data or information resource, service resource, database | Database of different optogenetics resources like hardware, protocols, sequence information. | Optogenetic, data | has parent organization: Stanford University; Stanford; California | Free, Freely available | SCR_017513 | 2026-08-14 09:27:47 | 2 | ||||||||||
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Estimation Stats Resource Report Resource Website 10+ mentions |
Estimation Stats (RRID:SCR_018321) | service resource, analysis service resource, production service resource | Web application for data analysis and visualizing effect sizes. Data analysis with estimation graphics. | Data analysis, estimation graphics, visualizing effect sizes | PMID:31217592 | Free, Freely available | SCR_018321 | Estimation Statistics | 2026-08-14 09:27:52 | 34 | |||||||||
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Diabetes Biobank Brussels Resource Report Resource Website |
Diabetes Biobank Brussels (RRID:SCR_015571) | DBB | biomaterial supply resource, tissue bank, material resource | Non-profit initiative of the Belgian Diabetes Registry (BDR), the Beta Cell Therapy consortium (BCT), the Flemish Center for Medical Innovation (CMI) and the Brussels Institute for Research and Innovation (Innoviris). It aims to support medical research into the epidemiology, prevention, diagnosis and treatment of diabetes. | diabetes, non-profit, epidemiology, disease prevention | Freely Available, Account required, Acknowledgement requested | SCR_015571 | Diabetes Biobank Brussels (DBB) | 2026-08-14 09:27:16 | 0 | |||||||||
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RefLib Resource Report Resource Website |
RefLib (RRID:SCR_018320) | data access protocol, software resource, application programming interface | Reference library processing for JavaScript. Reference library processing for NodeJS. | Reference library processing, Java script, NodeJS, citation, citation record, data | Free, Available for download, Freely available | SCR_018320 | Reflib-Node | 2026-08-14 09:28:01 | 0 | ||||||||||
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Healthcare Cost and Utilization Project Resource Report Resource Website 100+ mentions |
Healthcare Cost and Utilization Project (RRID:SCR_024410) | HCUP | data or information resource, portal, organization portal | Family of healthcare databases and related software tools and products developed through Federal-State-Industry partnership. Databases bring together data collection of State data organizations, hospital associations, private data organizations, and Federal government to create national information resource of encounter-level healthcare data. HCUP includes largest collection of longitudinal hospital care data in the United States, with all-payer, encounter-level information beginning in 1988. These databases enable research on broad range of health policy issues, including cost and quality of health services, medical practice patterns, access to healthcare programs, and outcomes of treatments at the national, State, and local market levels. | HCUP Databases, HCUP Tools and Software, healthcare data, healthcare databases, healthcare software tools and products, State data organizations, hospital associations, private data organizations, Federal government, create national information resource, hospital care data, | Agency for Healthcare Research and Quality | Free, Freely available | SCR_024410 | 2026-08-14 09:28:47 | 124 | |||||||||
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Trail Technical Report Archive Resource Report Resource Website |
Trail Technical Report Archive (RRID:SCR_017324) | TRAIL | data or information resource, service resource, database | Repository of technical reports from US government. Identifies, acquires, catalogs, digitizes and provides unrestricted access to U.S. government agency technical reports. Ensures preservation, discoverability, and persistent open access to government technical publications regardless of form or format. Search interface is hosted by University of Washington and searches all TRAIL content found at HathiTrust and UNT. | repository, technical, report, US government, agency | is related to: University of Washington; Seattle; USA | Free, Freely available | SCR_017324 | Technical Report Archive and Image Library | 2026-08-14 09:27:45 | 0 | ||||||||
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BrainRegionMarkers Resource Report Resource Website |
BrainRegionMarkers (RRID:SCR_023836) | source code, software toolkit, software resource | Software R package provides matrix of predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas. | Allen Human Brain Atlas, predefined set of marker genes matrix, human brain regions, human brain, | is related to: Allen Institute for Brain Science | Free, Freely available | SCR_023836 | 2026-08-14 09:28:59 | 0 | ||||||||||
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University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility Resource Report Resource Website |
University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) | MidSouth Bioinformatics Center, MBC | software resource, service resource, access service resource, core facility | Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice. | bioinformatics, assistance, consulting, training, analysis, omic, data | has parent organization: University of Arkansas; Arkansas; USA | Open | SCR_017168 | Bioinformatics Center, , University of Arkansas, UA, Core Facility, MBC, UALR, MidSouth, Little Rock | 2026-08-14 09:27:33 | 0 | ||||||||
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GCEA_FalsePositives Resource Report Resource Website |
GCEA_FalsePositives (RRID:SCR_023835) | source code, software toolkit, software resource | Software toolbox for gene category enrichment analysis false positives available. Used for analysis of statistical biases in Gene Set Enrichment Analysis applied to transcriptomic atlas data. | Allen Mouse Brain Atlas, Allen Human Brain Atlas, Gene Set Enrichment Analysis, GSEA, gene category enrichment analysis, transcriptomic atlas data, analysis false positives, statistical biases, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023835 | 2026-08-14 09:29:08 | 0 | ||||||||||
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HmtVar Resource Report Resource Website 10+ mentions |
HmtVar (RRID:SCR_017288) | data or information resource, service resource, database | Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. | manually, curated, data, variability, mitochondria, pathogenicity, mtDNA, variant, human, bio.tools |
uses: HmtDB - Human Mitochondrial DataBase uses: 1000 Genomes Project and AWS uses: MITOMAP - A human mitochondrial genome database uses: MutPred uses: SNPsandGO is listed by: Debian is listed by: bio.tools is affiliated with: University of Bologna; Bologna; Italy has parent organization: University of Bari; Bari; Italy |
Rosa Maria Massari fellowship from the Italian Association for Cancer Research ; DHOMOS Worldwide Cancer Research ; DISCO TRIP ; Italian Ministry of Health |
PMID:30371888 PMID:31821723 |
Free, Freely available | biotools:HmtVar | https://bio.tools/HmtVar | SCR_017288 | 2026-08-14 09:27:44 | 12 | ||||||
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ABAnnotate Resource Report Resource Website |
ABAnnotate (RRID:SCR_023833) | source code, software toolkit, software resource | Software toolbox for ensemble-based multimodal gene-category enrichment analysis of human neuroimaging data.Performs ensemble-based gene-category enrichment analysis on volumetric human neuroimaging data via brain-wide gene expression patterns derived from Allen Human Brain Atlas. Utilizes nonparametric method using spatial autocorrelation-corrected phenotype null maps for estimation of gene-category null ensembles. | Allen Human Brain Atlas, human neuroimaging data analysis, gene expression patterns, volumetric human neuroimaging data, gene-category null ensembles estimation, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023833 | 2026-08-14 09:28:58 | 0 | ||||||||||
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fiddle Resource Report Resource Website 1+ mentions |
fiddle (RRID:SCR_017327) | FIDDLE | software application, service resource, software resource | Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community. | identify, publication, format, dataset, , result, file, drawer, data, liberation, effort | DOI:10.31219/osf.io/6mcu3 | Free, Freely available | https://github.com/quest-bih/FIDDLE | SCR_017327 | file drawer data liberation effort, fiddle | 2026-08-14 09:27:35 | 2 | |||||||
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ROIs selection with a non-graphical user interface Resource Report Resource Website 1+ mentions |
ROIs selection with a non-graphical user interface (RRID:SCR_016352) | data access protocol, software resource, application programming interface | It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets. | non graphical, user, interface, keyboard, callback, function, analysis, big, data, set | is related to: MATLAB | Free, Available for download, Freely available | https://ptrrupprecht.wordpress.com/2015/06/24/a-simple-non-graphical-user-interface-in-matlab-keyboard-callback-functions/ | SCR_016352 | 2026-08-14 09:27:24 | 4 | |||||||||
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Atlas Densities Resource Report Resource Website |
Atlas Densities (RRID:SCR_023839) | source code, software toolkit, software resource | Software tools to compute densities in context of brain atlases. Used to create BBP Cell Atlas, using Allen Mouse Brain Atlas and collected literature density values.Provides list of volumetric files that provides cell type density estimates for each voxel of mouse brain volume. | Allen Mouse Brain Atlas, compute densities in context of brain atlases, create BBP Cell Atlas, collected literature density values, list of volumetric files, mouse brain volume, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023839 | 2026-08-14 09:28:59 | 0 | ||||||||||
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Phi Toolbox Resource Report Resource Website 1+ mentions |
Phi Toolbox (RRID:SCR_015549) | source code, software toolkit, software resource | Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation. | matlab, integrated information, phi, Φ, neural data, computation | PMID:26796119 PMID:27930289 |
Open Source, Available for download | SCR_015549 | Φ toolbox, phi toolkit, integrated information matlab toolbox | 2026-08-14 09:27:25 | 1 | |||||||||
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Kidney Interactive Transcriptomics Resource Report Resource Website 50+ mentions |
Kidney Interactive Transcriptomics (RRID:SCR_017209) | KIT | data or information resource, service resource, analysis service resource, production service resource | Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website. | Analyzer, kidney, single, cell, dataset, gene, expression, mouse, human, organoid | Free, Freely available | https://www.rebuildingakidney.org/ | SCR_017209 | 2026-08-14 09:28:00 | 99 | |||||||||
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EGSEA Resource Report Resource Website 50+ mentions |
EGSEA (RRID:SCR_015036) | source code, software toolkit, software resource | Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. | gene set, rna sequencing, analysis method, r package, bio.tools |
is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
Victorian State Government Operational Infrastructure Support ; Australian Government NHMRC IRIISS ; NHMRC GNT1050661; NHMRC GNT1045936; NHMRC GNT1057854; NHMRC GNT1104924 |
PMID:27694195 | Free, Available for download | biotools:egsea | https://bio.tools/egsea | SCR_015036 | Ensemble of Gene Set Enrichment Analyses (EGSEA), Ensemble of Gene Set Enrichment Analyses | 2026-08-14 09:27:03 | 64 | |||||
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Atlas Alignment Meter Resource Report Resource Website |
Atlas Alignment Meter (RRID:SCR_023843) | source code, software toolkit, software resource | Software Python CLI and library to measure jaggyness of brain parcellation volume. Used to measure slice-to-slice jaggedness of volumetric dataset, only in form of NRRD file. | Allen Mouse Brain Atlas, measure jaggyness of brain parcellation volume, volumetric dataset, volumetric dataset jaggedness, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023843 | 2026-08-14 09:28:42 | 0 | ||||||||||
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KEGG PATHWAY Database Resource Report Resource Website 1000+ mentions |
KEGG PATHWAY Database (RRID:SCR_018145) | data or information resource, service resource, database | Reference database for pathway mapping in KEGG Mapper. Collection of manually drawn pathway maps representing knowledge on molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organisms systems, human diseases, drug development. | Pathway mapping, reference database, KEGG Mapper, molecular interaction, reaction and relation network, metabolism, genetic information processing, cellular process, organism system, human disease, drug development, data | is related to: KEGG | Free, Freely available | SCR_018145 | KEGG PATHWAY | 2026-08-14 09:27:58 | 1224 | |||||||||
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Embassy-domsearch Resource Report Resource Website |
Embassy-domsearch (RRID:SCR_016086) | source code, software toolkit, software resource | Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt. | dhf, daf, redundancy, protein, domain, psi-blast, uniprot, molecular, biology |
is used by: RAVEN is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/embassy-domsearch/ | SCR_016086 | 2026-08-14 09:27:35 | 0 |
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