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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Michigan Imputation Server Resource Report Resource Website 1+ mentions |
Michigan Imputation Server (RRID:SCR_023554) | data access protocol, software resource, web service | Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4. | Genotype imputation, whole genotype imputation workflow, parallelization of computationally intensive tasks, | is related to: MINIMAC | NHGRI HG007022; NHLBI HL117626; NHGRI HG000376; NIDA R01DA037904; Austrian Science Fund ; European Community Seventh Framework Programme ; NIA |
PMID:27571263 | Free, Freely available | https://github.com/genepi/imputationserver | SCR_023554 | 2026-02-13 10:58:59 | 8 | |||||||
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scite Resource Report Resource Website 1+ mentions |
scite (RRID:SCR_018568) | text extraction software, data or information resource, service resource, software application, software resource | Web tool to classify citation statements from scientific articles using deep learning. Used for discovering and evaluating scientific articles via Smart Citations. | Classify citation statement, context, text extraction, deep learning, citation context, cited claim evidence, ASWG | NIDA R44 DA050155; NSF |
Restricted | SCR_018568 | 2026-02-13 10:58:13 | 2 | ||||||||||
|
Minian Resource Report Resource Website 1+ mentions |
Minian (RRID:SCR_022601) | data processing software, data analysis software, software toolkit, software application, software resource | Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output. | Miniscope, analysis pipeline, calcium imaging, mouse, Visualization, OpenBehavior |
is listed by: OpenBehavior has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NIMH DP2MH122399; NIMH R01MH120162; NIBIB R01EB028166; NSF 1926800; NSF 2046583; NINDS U01NS094286; NSF 1700408; NIA F32AG067640; NINDS R03 NS111493; NIDA R21 DA049568; NINDS R01 NS116357 |
PMID:35642786 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/minian/ | SCR_022601 | 2026-02-13 10:58:45 | 4 | |||||||
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simple-t1-motion-detection Resource Report Resource Website |
simple-t1-motion-detection (RRID:SCR_016022) | software resource, image analysis software, data processing software, software application | Software to measure the amount of ghosting artifacts in T1-weighted DICOM images. This program reads DICOM images and calculates a measure of the noise structure in one part of the image. | measure, read, image, calculate, noise, structure, part, digital, medicine, information, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016022 | 2026-02-13 10:57:39 | 0 | |||||||||
|
Spark Resource Report Resource Website 100+ mentions |
Spark (RRID:SCR_006207) | Spark | data visualization software, data processing software, data analysis software, software application, software resource | A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality. | epigenomics, genome browser, clustering, visualization, genome, computation, pattern discovery, cluster |
is related to: Genboree Discovery System is related to: Roadmap Epigenomics Project has parent organization: BC Cancer Agency |
Canadian Institutes of Health Research ; Michael Smith Foundation for Health Research ; Natural Sciences and Engineering Research Council of Canada ; NIDA U01 DA025956; NIEHS 5U01ES017154-02; NHGRI HG004558 |
PMID:22960372 | Available for download without charge. Please cite. | nlx_151753 | SCR_006207 | Sparkinsight | 2026-02-13 10:55:47 | 403 | |||||
|
Antibody Registry Resource Report Resource Website 100+ mentions |
Antibody Registry (RRID:SCR_006397) | data repository, storage service resource, data or information resource, service resource, database | Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications. The registry contains antibody product information organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones). Data is provided in many formats so that authors of biological papers, text mining tools and funding agencies can quickly and accurately identify the antibody reagents they and their colleagues used. The Antibody Registry allows any user to submit a new antibody or set of antibodies to the registry via a web form, or via a spreadsheet upload. | RIN, Resource Information Network, antibody, reagent, unique identifiers, RRID Community Authority, |
is used by: Resource Identification Portal is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is listed by: OMICtools is listed by: FORCE11 is listed by: re3data.org is listed by: Resource Information Network is related to: Novus Biologicals is related to: DOMEO is related to: Journal of Comparative Neurology Antibody database is related to: Integrated Manually Extracted Annotation has parent organization: Neuroscience Information Framework |
NIDA ; NIH Blueprint for Neuroscience Research ; U.S. Department of Health and Human Services HHSN27120080035C |
Creative Commons Attribution License, The community can contribute to this resource | biodbcore-000182, nif-0000-07730, OMICS_01768, r3d100010408 | https://doi.org/10.17616/R3XG7N | SCR_006397 | AntibodyRegistry, AB Registry, The Antibody Registry, ABRegistry | 2026-02-13 10:55:51 | 109 | ||||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | data access protocol, software resource, web service, web application | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NIAAA U01 AA016662; NIAAA U01 AA013512; NIDA P01 DA015027; NIMH P50 MH078028; NIMH P50 MH096972; NCI U24 CA159988; NIGMS R01 GM088822 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-02-13 10:55:56 | 2760 | ||||
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Phenotypes and eXposures Toolkit Resource Report Resource Website 50+ mentions |
Phenotypes and eXposures Toolkit (RRID:SCR_006532) | PhenX Toolkit | catalog, data set, data or information resource, service resource, narrative resource, database, standard specification | Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols. | PhenX project, genome, phenotype, genome-wide association study, genetic variation, genomic study, substance abuse, addiction, substance use, environmental exposure, disease susceptibility, outcome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: RTI International has parent organization: Consensus Measures for Phenotype and Exposure has parent organization: Trans-Omics for Precision Medicine (TOPMed) Program has organization facet: PhenX Phenotypic Terms is organization facet of: Consensus Measures for Phenotype and Exposure |
NHGRI U01 HG004597; NHGRI U41HG007050; NIDA ; OBSSR ; NIMH ; NHLBI ; NIMHD ; TRSP ; NHGRI U24 HG012556; ODP ; NINDS ; NCI |
PMID:21749974 | Restricted | SCR_017475, biotools:PhenX_toolkit, nlx_144102 | https://bio.tools/PhenX_Toolkit | SCR_006532 | Phenotypes and eXposures Toolkit | 2026-02-13 10:55:50 | 61 | ||||
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Transdisciplinary Tobacco Use Research Centers Resource Report Resource Website |
Transdisciplinary Tobacco Use Research Centers (RRID:SCR_006858) | TTURC | disease-related portal, data or information resource, portal, topical portal | A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment. | gene, genetic factor, addiction gene, behavioral treatment, biomarker, molecule, nicotine use disorder, prevention, psychosocial factor, smoking, smoking cessation, tobacco exposure, treatment, nicotine, prevention, tobacco, intervention | has parent organization: National Cancer Institute | Nicotine use disorder, Addiction | NCI ; NIDA ; NIAAA |
nif-0000-24133 | SCR_006858 | 2026-02-13 10:55:54 | 0 | |||||||
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FMRIB’s Integrated Registration and Segmentation Tool Resource Report Resource Website 1+ mentions |
FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) | FIRST | registration software, data processing software, data analysis software, software application, segmentation software, software resource, image analysis software | Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences. | Functional Magnetic Resonance Imaging of the Brain, segmentation, registration, volumetric segmentation, performing vertex analysis, |
is related to: Multimodal Image Segmentation Tool is a plug in for: FSL |
NCRR P41 RR14075; NINDS R01 NS052585; NCRR R01 RR16594; NIMH K08 MH01573; NIMH K01 MH01798; NIDA R01 DA017905 |
PMID:21352927 | Free, Freely available | SCR_024921 | , Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool | 2026-02-13 10:59:19 | 2 | ||||||
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delay-discounting Resource Report Resource Website |
delay-discounting (RRID:SCR_016031) | software resource, software application | Software that performs a delay-discounting task measuring impulsivity. Used in ABCD study. | abcd, delay, discounting, task, measure, impulsivity, software, application, tool | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016031 | 2026-02-13 10:57:45 | 0 | |||||||||
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The Experiment Factory Resource Report Resource Website 1+ mentions |
The Experiment Factory (RRID:SCR_016107) | software resource, software application | Software that generates container-based behavioral experiments for reproducible science. It offers a library of experiments, games, and surveys, support for multiple kinds of databases, and robust documentation for the provided tools. | docker, psychology, behavior, experiment, container, reproducibility, reproducibility, database, library, documentation | NIDA UH2 DA041713; William R. Hewlett Stanford Graduate Fellowship ; National Science Foundation ; NIDA F32DA041773 |
PMID:27199843 | Free, Available for download | SCR_016107 | EXPFACTORY | 2026-02-13 10:57:45 | 1 | ||||||||
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CRAPome Resource Report Resource Website 10+ mentions |
CRAPome (RRID:SCR_025008) | web service, data or information resource, data access protocol, software resource, database | Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions. | Mass Spectrometry contaminants, standardized negative controls, contaminant repository, AP-MS analysis, affinity purification, mass spectrometry data, | NIGMS 5R01GM94231; NIDA DP1DA026192; NHLBI HL112618-01; Canadian Institutes of Health Research ; government of Ontario ; Austrian Academy of Sciences ; Austrian Federal Ministry for Science and Research ; European Research Council ; Austrian Science Fund ; European Molecular Biology Organisation ; Netherlands Proteomics Center ; European Union 7th Framework Program ; Stowers Institute for Medical Research ; Human Frontier Science Program ; NCI R21 CA16006001A1 |
PMID:23921808 | Free, Freely available, | https://reprint-apms.org/ | SCR_025008 | CRAPome:Contaminant Repository for Affinity Purification | 2026-02-13 10:59:26 | 16 | |||||||
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Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software resource, source code, software toolkit | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-02-13 10:59:46 | 1 |
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