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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-07-28 09:44:26 | 111 | ||||||
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GEROprotectors Resource Report Resource Website 10+ mentions |
GEROprotectors (RRID:SCR_016737) | data or information resource, database | Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases. | geroprotector, data, collection, current, thearpeutic, prevention, aging, disease, geriatic |
uses: PubChem uses: ChemSpider uses: DrugBank uses: ChEMBL uses: CHEBI uses: UniProt uses: GenAge |
Wellcome Trust ; Israel Ministry of Science and Technology ; Fund in Memory of Dr. Amir Abramovich |
PMID:26342919 | Public, Free, Freely available | SCR_016737 | Geroprotectors | 2026-07-28 09:44:26 | 11 | |||||||
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COLLECT database Resource Report Resource Website 1+ mentions |
COLLECT database (RRID:SCR_018366) | data or information resource, database | Collaborative database for pregnancy and placental research studies worldwide by Global Pregnancy Collaboration CoLab . Database for collecting data for pregnancy studies in preeclampsia and other fields. Database has web based data entry platform with study specific user access. Data can also be entered offline using formatted spreadsheet template that can be uploaded to database in bulk or stored locally. Data is property of investigator but with permission can be combined into larger studies across centers and countries. Collaboration is enabled but not required. | Placenta, preeclampsia, obstetrics, perinatal research, data, data set, pregnancy, Global Pregnancy Collaboration, CoLab | preeclampsia | Bill and Melinda Gates Foundation | PMID:29978556 PMID:28864015 |
Restricted | SCR_018366 | 2026-07-28 09:44:55 | 1 | ||||||||
|
Molecular Signatures Database Resource Report Resource Website 500+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NIH ; NIGMS ; NCI CA295532 |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-07-28 09:44:28 | 762 | ||||||
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Cocoframer Resource Report Resource Website |
Cocoframer (RRID:SCR_023817) | software toolkit, software resource | Software R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer. | Allen Mouse Brain Atlas, Common Coordinate Framework, retrieving 3D, CCF aligned, gridded ISH, data, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023817 | COmmon COordinate FRAMEwork in R | 2026-07-28 09:45:58 | 0 | |||||||||
|
VA Phenomics Library Resource Report Resource Website 1+ mentions |
VA Phenomics Library (RRID:SCR_019107) | VAPheLib | data or information resource, database | Shared knowledgebase of VA EHR-based phenotype algorithms, definitions and data curation metadata. | Phenomics library, centralized phenomics VA library, data, curation metadata, phenotype | https://www.hsrd.research.va.gov/for_researchers/cyber_seminars/archives/3814-notes.pdf | SCR_019107 | 2026-07-28 09:44:55 | 1 | ||||||||||
|
Research Information Network Resource Report Resource Website |
Research Information Network (RRID:SCR_000931) | data or information resource, narrative resource | A network resource that aims to enhance and broaden understanding of how researchers in the UK create and use information resources. The network provides services of all kinds to support the development of effective policies and practices for researchers, institutions, funders, information professionals and everyone who is involved in the information landscape. | information, data, network | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_77489 | http://www.rin.ac.uk/blogs/team | SCR_000931 | Research Information Network | 2026-07-28 09:40:09 | 0 | ||||||||
|
elmr Resource Report Resource Website |
elmr (RRID:SCR_017249) | software toolkit, software resource | 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 | 2026-07-28 09:44:32 | 0 | |||||||||
|
metagear Resource Report Resource Website |
metagear (RRID:SCR_017085) | software toolkit, software resource | 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 | 2026-07-28 09:44:31 | 0 | |||||||
|
clustLasso Resource Report Resource Website 1+ mentions |
clustLasso (RRID:SCR_018820) | software toolkit, software resource | Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach. | Predictive signatures, microbial phenotype, cluster lasso approach, build predictive signature, phenotype, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:clustlasso | https://bio.tools/clustlasso | SCR_018820 | 2026-07-28 09:44:50 | 1 | ||||||||
|
ODDPub Resource Report Resource Website 1+ mentions |
ODDPub (RRID:SCR_018385) | software resource, algorithm resource | Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature. | Text mining, biomedical publication screening, data sharing statement detection, open data, open code, publication, data, biomedical literature, Berlin Institute of Health, ASWG | is used by: rtransparent | Free, Available for download, Freely available | SCR_018385 | 2026-07-28 09:44:40 | 5 | ||||||||||
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DDRTree Resource Report Resource Website 1+ mentions |
DDRTree (RRID:SCR_026795) | software toolkit, software resource | Software R package provides implementation of framework of reversed graph embedding which projects data into reduced dimensional space while constructs principal tree which passes through middle of data simultaneously. | reversed graph embedding, data, reduced dimensional space, constructs principal tree, | Free, Available for download, Freely available | SCR_026795 | DDRTree: Learning Principal Graphs with DDRTree | 2026-07-28 09:46:46 | 2 | ||||||||||
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plyr Resource Report Resource Website 1+ mentions |
plyr (RRID:SCR_026985) | software toolkit, software resource | Software R package for splitting, applying and combining data. Used to split up big data structure into homogeneous pieces, apply function to each piece and then combine all the results back together. | splitting, applying, combining, data | Free, Available for download, Freely available | https://github.com/hadley/plyr | SCR_026985 | 2026-07-28 09:46:55 | 1 | ||||||||||
|
Mammal Diversity Database Resource Report Resource Website 1+ mentions |
Mammal Diversity Database (RRID:SCR_026173) | data or information resource, database | Updatable online database of mammal taxonomic and biodiversity information hosted by American Society of Mammalogists. Provides information on species-level and higher taxonomic changes, thereby promoting more rigorous study of mammalian biodiversity worldwide. The initial objective has been to aggregate, curate, and compile, new citations on species descriptions and taxonomic revisions into regular releases that are downloadable in comma-delimited format. Downstream goals include expanded hosting of ecological, trait, and taxonomic data. | American Society of Mammalogists, mammal, taxonomic, biodiversity, information, ecological, trait, taxonomic, data | Free, Freely available, | https://zenodo.org/records/4139818 | SCR_026173 | 2026-07-28 09:46:33 | 2 | ||||||||||
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Research Accelerator Resource Report Resource Website 1+ mentions |
Research Accelerator (RRID:SCR_006051) | UCSD Research Accelerator | service resource, portal, data or information resource, community building portal, database | Software platform that allows researchers to easily collaborate on research and share reagents, antibodies, cell lines and more. It is designed to increase scientific collaboration across disciplines and geographical boundaries. Among the institutions now using the platform include Yale University, U of Pennsylvania, U of Chicago, Washington U, Cambridge University, University College London. The platform is licensed to select institutions. ResearchAccelerator.org allows researchers to form targeted, data driven collaborations. Researchers can search for data based on gene, disease and pathway, and they can post data which would otherwise be orphaned. The resulting collaborations, which are likely to be transdisciplinary, can greatly amplify impact and research productivity. | collaboration, transdisciplinary research, gene, pathway, disease, cell line, data, human sample, laboratory protocol, medical device, equipment, resource, reagent, research project, transgenic animal, knock out animal, validated antibody, yale keck proteomics assay, allergy, immunology, bone, joint, orthopedic, cancer, cardiovascular, gastroenterology, infectious disease, neurologic disease, organ transplantation, psychiatric disease, reproductive disease, vascular disease, sharing, material resource |
is used by: University College London; London; United Kingdom is used by: University of Cambridge; Cambridge; United Kingdom is used by: Washington University in St. Louis; Missouri; USA is used by: University of Chicago; Illinois; USA is used by: University of Pennsylvania; Philadelphia; USA is used by: Yale University; Connecticut; USA has parent organization: University of California at San Diego; California; USA |
Allergy, Immunology, Bone, Joint, Orthopedic, Cancer, Cardiovascular, Gastroenterology, Infectious Disease, Neurologic disease, Organ Transplantation, Psychiatric disease, Reproductive disease, Vascular disease | The community can contribute to this resource | nlx_151451 | SCR_006051 | ResearchAccelerator.org, ResearchAccelerator | 2026-07-30 09:27:18 | 1 | ||||||
|
Dryad Digital Repository Resource Report Resource Website 1000+ mentions |
Dryad Digital Repository (RRID:SCR_005910) | service resource, data repository, data or information resource, database, storage service resource | International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository. | international, digital, repository, curated, data, collection, scientific, medical, publication, dataset, FASEB list |
is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: CINERGI is listed by: re3data.org is listed by: Connected Researchers is listed by: DataCite is listed by: FAIRsharing is related to: ImpactStory is related to: Connected Researchers has parent organization: NESCent - National Evolutionary Synthesis Center has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: University of California; California; USA |
Institute for Museum and Library Services ; JISC ; NSF ; European Commission |
DOI:10.25504/FAIRsharing.wkggtx, DOI:10.5061, r3d100000044, DOI:10.15146, DOI:10.17616/R34S33, nlx_149486 | https://doi.org/10.17616/R34S33, https://doi.org/10.5061/, https://doi.org/10.15146, https://dx.doi.org/10.5061/, https://dx.doi.org/10.15146, https://fairsharing.org/10.25504/FAIRsharing.wkggtx, https://api.datacite.org/dois?prefix=10.18736, https://api.datacite.org/dois?prefix=10.6076, , https://doi.org/10.17616/R34S33 | http://www.datadryad.org/ | SCR_005910 | , The Dryad Digital Repository, Dryad Digital Repository, Dryad | 2026-07-30 09:27:15 | 2535 | ||||||
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MITRE Neuroinformatics Resource Report Resource Website |
MITRE Neuroinformatics (RRID:SCR_006508) | MITRE Neuroinfomatics | data processing software, data transfer software, data distribution software, data analysis software, data visualization software, simulation software, software resource, software application | This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality. | brain, data, diffusion tensor image, distorted, human, imagery, image, informatics, investigator, laboratory, magnetic resonance image, mapping, neuroscience, structural, visualization, neuroimaging | Human Brain Project ; MITRE Technology Program ; NSF ; NIMH R01-MH64417 |
nif-0000-10469 | http://neuroinformatics.mitre.org/ | SCR_006508 | Neuroinfomatics at MITRE, Neuroinformatics: Exploring the Human Brain | 2026-07-30 09:27:24 | 0 | |||||||
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Phantom Camera Control Resource Report Resource Website 1+ mentions |
Phantom Camera Control (RRID:SCR_021080) | PCC | data processing software, software application, data analysis software, software resource | Software application for Phantom cameras. Controls every camera function on every Phantom camera model. Fine-tune resolution, frame rate, exposure, memory segmentation, trigger modes and automatic functions prior to recording. PCC also makes it easy to work with synchronized cameras, manage Phantom Cine raw files and convert files to format for final project.Software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems. | Phantom, Phantom camera, image, data, processing, raw files, convert files | Free, Available for download, Freely available | SCR_021080 | 2026-07-30 09:30:55 | 1 | ||||||||||
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PICS Resource Report Resource Website 1+ mentions |
PICS (RRID:SCR_001093) | data processing software, sequence analysis software, data analysis software, software resource, software application | R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach. | chip seq, bayes, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20528864 | Free, Available for download, Freely available | OMICS_00455 | SCR_001093 | Probabilistic inference of ChIP-seq | 2026-07-30 09:26:05 | 3 | |||||||
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Clonotator Resource Report Resource Website |
Clonotator (RRID:SCR_016730) | data processing software, sequence analysis software, data access protocol, data analysis software, software resource, web service, image analysis software, alignment software, software application | Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data. | screening, annotation, cDNA, sequence, amino acid, align, reference, database, protein, disease, mutation, transcriptomic, data | has parent organization: University of California at San Francisco; California; USA | Free, Freely available, Registration required | https://willseylab.com/clonotator/ | SCR_016730 | 2026-07-30 09:30:03 | 0 |
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