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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Atlas of Drosophila Development Resource Report Resource Website |
Atlas of Drosophila Development (RRID:SCR_017506) | data or information resource, atlas | Collection of color illustrations that follow main events of embryogenesis and post embryonic development of Drosophila. | Color, illustration, embrogenesis, post, embryonic, development, Drosophila, data | Free, Freely available | SCR_017506 | 2026-02-16 09:49:15 | 0 | |||||||||||
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RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | service resource, data or information resource, database | Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature. | Annotate, SNP, regulatory, DNA, element, intergenic, region, human, genome, sequence, DNAase, hypersensitivity, binding, site, transcription, factor, promoter, region, data, FASEB list | NHGRI U54 HG 004558; Beta Cell Consortium |
PMID:22955989 | Free, Freely available | SCR_017905 | 2026-02-16 09:49:22 | 123 | |||||||||
|
CoMeTa Website Resource Report Resource Website 1+ mentions |
CoMeTa Website (RRID:SCR_017357) | CoMeTa | service resource, data or information resource, database | Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions. | Interactive, database, miRNA, target, gene, network, integrate, expression, condition, pathway, functional, data | Italian Telethon Foundation ; AIRC |
PMID:22345618 | Free, Freely available | SCR_017357 | Co-expression Meta-analysis of miRNA Target | 2026-02-16 09:49:13 | 3 | |||||||
|
ABA Mouse Brain: Atlas Resource Report Resource Website 100+ mentions |
ABA Mouse Brain: Atlas (RRID:SCR_017479) | service resource, data or information resource, database | Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain. | Genome, data, gene, expression, mouse, brain |
has parent organization: Allen Institute for Brain Science is provided by: Allen Brain Atlas |
PMID:17151600 | Free, Freely available | SCR_017479 | Allen Brain Atlas: Mouse Brain, , Allen Brain Atlas Mouse Brain: Atlas | 2026-02-16 09:49:15 | 328 | ||||||||
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Geno2MP Resource Report Resource Website 1+ mentions |
Geno2MP (RRID:SCR_016872) | Geno2MP | service resource, data or information resource, database | Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community. | data, collection, Mendelian, phenotype, affected, individuals, profile, human, genetics |
is used by: MARRVEL is listed by: OMICtools |
University of Washington Center for Mendelian Genomics ; Seattle ; WA |
Free, Available for download, Freely available | SCR_016872 | Geno2MP, 2 Mendelian Phenotype, The Genotype 2 Mendelian Phenotype database | 2026-02-16 09:49:06 | 2 | |||||||
|
mousebrain.org Resource Report Resource Website 100+ mentions |
mousebrain.org (RRID:SCR_016999) | data or information resource, atlas | Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system. | Atlas, brain cell, cell type, single cell RNA seq data, taxon, tissue, gene, marker, anatomical location, data | has parent organization: Karolinska Institute; Stockholm; Sweden | Knut and Alice Wallenberg Foundation ; Swedish Foundation for Strategic Research ; Wellcome Trust ; Swedish Research Council ; SSF ; Cancerfonden ; EU ; Hjärnfonden ; SFO Strat Regen ; European Research Council ; Ollie and Elof Ericssons Foundation ; Åke Wiberg Foundation |
PMID:30096314 | Free, Available for download, Freely available | SCR_018356 | SCR_016999 | Linnarsson lab Mouse Brain Atlas | 2026-02-16 09:49:08 | 111 | ||||||
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ResistomeDB Resource Report Resource Website 1+ mentions |
ResistomeDB (RRID:SCR_018305) | service resource, data or information resource, database | Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class. | Antibiotic Resistance Gene, Tara Oceans, data, antibiotic resistance, antibiotic, gene | DOI:10.1101/765446 | Free, Freely available | SCR_018305 | 2026-02-16 09:49:29 | 1 | ||||||||||
|
DREME Resource Report Resource Website 10+ mentions |
DREME (RRID:SCR_016860) | production service resource, service resource, data analysis service, analysis service resource | Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences). | discover, short, ungapped, motif, sequence, compare, shuffled, control, sample, output, recurring, fixed, length, pattern, data | is listed by: MEME Suite - Motif-based sequence analysis tools | Free, Available for download, Freely avaialble | SCR_016860 | Discriminative Regular Expression Motif Elicitation, DREME | 2026-02-16 09:49:06 | 20 | |||||||||
|
Cerebellar Platform Resource Report Resource Website 1+ mentions |
Cerebellar Platform (RRID:SCR_001700) | Cerebellar Platform | software repository, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation. | electrophysiology, function, analysis, cerebellar, data, imaging, mathematical, model, molecular biology, paper, plasticity, program, review, script, structure, theory, book, cerebellum |
is used by: NIF Data Federation is related to: Integrated Software has parent organization: RIKEN Brain Science Institute |
Japan Society for the Promotion of Science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10193 | SCR_001700 | 2026-02-16 09:45:33 | 1 | |||||||
|
Statistical Analysis System Resource Report Resource Website 5000+ mentions |
Statistical Analysis System (RRID:SCR_008567) | SAS | software application, software resource, data analytics software, data management software | Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS. | Explore, analyze, visualize, data, standardized, management, statistics | is listed by: SoftCite | Restircted | nif-0000-31484 | https://www.sas.com/en_us/software/platform.html https://www.sas.com/en_us/software/sas9.html |
SCR_008567 | Statistical Analysis System, SAS Intelligence Platform, SAS 9.4 | 2026-02-16 09:47:13 | 7165 | ||||||
|
STATISTICA Resource Report Resource Website 5000+ mentions |
STATISTICA (RRID:SCR_014213) | software application, software resource, data analytics software | Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures. | TIBCO, statistical, test, data, mining, |
is listed by: Metabolomics Workbench is listed by: SoftCite |
Commercially available, Free download available | http://statistica.software.informer.com/10.0/ http://statistica.io/products/ |
SCR_014213 | Statistica 10, STATISTICS Product Index, Statistica | 2026-02-16 09:48:32 | 7864 | ||||||||
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elmr Resource Report Resource Website |
elmr (RRID:SCR_017249) | software resource, software toolkit | Software tool as support for working with light and electron microscopy fly brain data. Part of suite of R packages based on NeuroAnatomy Toolbox. Provides tools to move between adult brain EM and light level data, emphasising interaction between CATMAID web application and R Neuroanatomy Toolbox package. | support, working, light, electron, microscopy, fly, brain, data | is related to: NeuroAnatomy Toolbox | Free, Available for download, Freely available | https://jefferis.github.io/elmr/ | SCR_017249 | 2026-02-16 09:49:11 | 0 | |||||||||
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metagear Resource Report Resource Website |
metagear (RRID:SCR_017085) | software resource, software toolkit | Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis. | sythesis, taxonomy, systematic, review, assemble, screen, literature, extract, meta, data, analysis, statistical |
is listed by: CRAN is related to: R Project for Statistical Computing has parent organization: University of South Carolina; South Carolina; USA |
NSF DBI-1262545; NSF DEB-1451031 |
DOI:10.1111/2041-210X.12472 | Free, Available for download, Freely available | https://github.com/cran/metagear https://lajeunesse.myweb.usf.edu |
SCR_017085 | 2026-02-16 09:49:09 | 0 | |||||||
|
CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | software application, software resource, data analytics software | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
Doris Duke Charitable Foundation ; Damon Runyon Cancer Research Foundation ; B&J Cardan Oncology Research Fund ; Ludwig Institute for Cancer Research ; NCI U01 CA154969; NIAID U19 AI090019; NCI T32 CA09302; US Department of Defense ; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-02-16 09:49:07 | 1239 | ||||||
|
California Coastal Atlas Resource Report Resource Website |
California Coastal Atlas (RRID:SCR_024554) | data or information resource, topical portal, portal | Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes. | California coast, water, climate, coastal processes, data, informing public policy, |
is listed by: DataCite has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.4246 | SCR_024554 | 2026-02-16 09:50:44 | 0 | |||||||||
|
Allen Mouse Brain Reference Atlas Resource Report Resource Website 100+ mentions |
Allen Mouse Brain Reference Atlas (RRID:SCR_002978) | ABA, ARA, ABA Mouse Brain | reference atlas, data or information resource, atlas | Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer. | 3D, map, gene, expression, data, adult, mouse, brain, interactive, image |
is used by: NIF Data Federation is used by: BICCN is related to: BrainStars is related to: PubAnatomy is related to: Integrated Brain Gene Expression is related to: Allen Brain Atlas API is related to: 3DBar is related to: aGEM is related to: CellTax vignette is related to: Blue Brain Cell Atlas is related to: Allen Mouse Brain Common Coordinate Framework is related to: SHARCQ is related to: Enhancer Trap Line Browser is related to: Linked Neuron Data has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas works with: MeshView works with: Brain Gene Expression Analysis toolbox works with: VisuAlign works with: MIRACL |
Free, Freely available | SCR_013286, nlx_21010, nif-0000-00508 | http://mouse.brain-map.org/atlas/index.html, http://mouse.brain-map.org/ | SCR_002978 | Allen Mouse Brain Reference Atlas, Allen Reference Atlases, ABA Adult Mouse Brain, ARA ontology | 2026-02-16 09:45:58 | 444 | ||||||
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BioJava Project Resource Report Resource Website 50+ mentions |
BioJava Project (RRID:SCR_007180) | BioJava | data processing software, software application, software resource | Project dedicated to providing Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. Sponsor: BioJava is not formally funded by any grants. Through the OBF they have received sponsorship from Sun Microsystems, Apple Computers and NESCent. The initial development of the phylogenetics module was undertaken as a Google Summer of Code 2007 project in collaboration with NESCent. | biojava, framework, biological, data, analytical, statistical, file, manipulation, 3d structure, application, bioinformatics |
is listed by: Debian is listed by: OMICtools |
OMICS_04848, nif-0000-30181 | https://sources.debian.org/src/libbiojava4-java/ | SCR_007180 | The BioJava Project, BioJava Project | 2026-02-16 09:46:54 | 85 | |||||||
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Duke University Medical Center Neuropsychiatric Imaging Research Laboratory Resource Report Resource Website 1+ mentions |
Duke University Medical Center Neuropsychiatric Imaging Research Laboratory (RRID:SCR_007124) | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Neuropsychiatric Imaging Research Laboratory (NIRL) analyze magnetic resonance images to research numerous psychiatric disorders including depression, bipolar disorder, and post traumatic stress disorder. NIRL also develop new methods for MR image processing to improve quality and reliability of research in the field of neuroimaging. The laboratory computer resources include Sun MicroSystems SPARC workstations, Windows PCs, over 3 terabytes of online hard disk space, and a web server system. The lab has a site filtered anonymous ftp server system for data transfer. There are individual offices for visiting fellows and analysts for image processing as well as shared work-study rooms and conference facilities. | allele, antioxidant, apolipoprotein-e, biomedical, bipolar, child, cognitive, data, depression, disorder, geriatric, hard disk, hiv, imaging, impairment, infection, magnetic resonance, magnetic resonance image, marijuana, mri, neurobiology, neurofibromatosis, neurological, neuropsychiatric, neuroscience, post traumatic stress disorder, prognostic, psychiatric, ptsd, research, server, terabyte, vascular, neuroimaging | has parent organization: Duke University; North Carolina; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10212 | http://nirlweb.mc.duke.edu/ | SCR_007124 | DMC NIRL | 2026-02-16 09:46:53 | 1 | |||||||
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UK Biobank Resource Report Resource Website 1000+ mentions |
UK Biobank (RRID:SCR_012815) | service resource, biobank, storage service resource, material storage repository | Biobank provides data collected at Assessment Center and via online questionnaires on participants aged 40-69 years recruited throughout United Kingdom and provides summary information to improve prevention, diagnosis and treatment of serious and life threatening illnesses. | Data, collected, United Kingdom, prevention, diagnosis, treatment, illness, questionnaire, blood, urine, saliva, cognitive function, psychological status, hearing test, interview, operation, medication, blood pressure, body measurementdie |
is listed by: One Mind Biospecimen Bank Listing is related to: AstraZeneca PheWAS Portal |
cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression, dementia. | UK Department of Health ; MRC ; Scottish Government ; Welsh Assembly Government ; Wellcome Trust |
grid.421945.f, nlx_95741, ISNI: 0000 0004 0396 0496, Wikidata: Q7864819 | https://ror.org/02frzq211 | SCR_012815 | 2026-02-16 09:48:18 | 2914 | |||||||
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Sanford Burnham Prebys Medical Discovery Institute X-ray Crystallography Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute X-ray Crystallography Facility (RRID:SCR_014860) | instrument supplier, material resource | Facility equipped with X-ray crystallography equipment, such as the Rigaku FR-E SuperBright Ultra high-intensity rotating anode generator. The instrument is inteded for self-usage by trained users. It utilizes both ports with two independent diffraction stations that can run simultaneously. Each station is equipped with an X-stream cryogenic system for standard low temperature (~100 K) data collection. The system is used to collect high resolution diffraction data from native and inhibitor-bound crystals or to test and optimize diffraction quality (cryo-protectant conditions, etc.) and screen for further data collection at synchrotron sources. | x ray, crystallography, diffraction, data, inhibitor-bound crystals, synchrotron | Commercially available | SCR_014860 | SBP X-ray Crystallography Facility, SBP Medical Discovery Institute X-ray Crystallography Facility | 2026-02-16 09:48:43 | 0 |
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