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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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biomod2 Resource Report Resource Website 50+ mentions |
biomod2 (RRID:SCR_018246) | software application, data processing software, data analysis software, software resource | Software R package for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization. | species distribution modeling, ensemble of models, ensemble forecasting, visualization, data | is listed by: CRAN | Free, Available for download, Freely available | SCR_018246 | 2026-02-15 09:22:19 | 55 | ||||||||||
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CNV webstore Resource Report Resource Website 1+ mentions |
CNV webstore (RRID:SCR_018007) | software application, data visualization software, data processing software, software resource, data storage software, software toolkit, data analysis software | Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. | Copy number variation, data, Illumina, CNV report, raw data, microarray data, clinical, analysis, visualization, gene prioritisation, PubMed searching, annotation, | Belgian National Fund for Scientific Research - Flanders ; Marguerite-Marie Delacroix foundation |
PMID:21208430 | http://cnv-webstore.ua.ac.be/cnv-webstore/ | SCR_018007 | CNV-webstore, CNV-WebStore | 2026-02-15 09:22:10 | 1 | ||||||||
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BioBank Central Resource Report Resource Website |
BioBank Central (RRID:SCR_008645) | BioBank Central | biospecimen repository, material storage repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. Web-based portal to connect all the constituencies in the global biobank community. The project seeks to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum. Biobanks are the meeting point of two major information trends in biomedical research: the generation of huge amounts of genomic and other laboratory data, and the electronic capture and integration of patient clinical records. They are comprised of large numbers of human biospecimens supplemented with clinical data. Biobanks when implemented effectively can harness the power of both genomic and clinical data and serve as a critical bridge between basic and applied research, linking laboratory to patient and getting to cures faster. As science and technology leaders work to address the many challenges facing U.S. biobanks logistical, technical, ethical, financial, intellectual property, and IT BioBank Central will serve as an accurate and timely source of knowledge and news about biorepositories and their role in research and drug development. The Web site also provides a working group venue, patient and public education programs, and a forum for international collaboration and harmonization of best practices. | biobank, community, biomedical, data, genomic, integration, patient, clinical, human, biospecimen, science, technology, biorepository, drug, development, education | has parent organization: Open Source Science Project | FasterCures ; Feinstein Kean Healthcare ; IBM Healthcare and Life Sciences ; Affymetrix ; Bioaccelerate Holdings Inc. ; Invitrogen Corporation |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-32933 | SCR_008645 | 2026-02-15 09:19:53 | 0 | |||||||
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GeneCluster 2: An Advanced Toolset for Bioarray Analysis Resource Report Resource Website 10+ mentions |
GeneCluster 2: An Advanced Toolset for Bioarray Analysis (RRID:SCR_008446) | software application, data processing software, software resource, software toolkit, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding supervised classification, gene selection, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbor (KNN) algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. It enhances the clustering capabilities of GeneCluster 1.0 by adding a module for batch SOM clustering, and also includes a marker gene finder based on a KNN analysis and a visualization module. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater. | gene, cluster, software, analysis, expression, bioarray, data, class, predictor, visualization, marker, classification, algorithm, module, java, environment | has parent organization: Broad Institute | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30293 | SCR_008446 | GeneCluster 2 | 2026-02-15 09:19:51 | 39 | ||||||||
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Rat Genome Database: Neurological Disease Portal Resource Report Resource Website 10+ mentions |
Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools. | gene, analysis, biological, data, database, disease, genome, model, neurological, neuroscience, pathway, phenotype, qtl, rat, research | has parent organization: Medical College of Wisconsin; Wisconsin; USA | Neurological disease | RGD ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33773 | http://rgd.mcw.edu | SCR_008685 | RGD Neurological Disease Portal | 2026-02-15 09:19:33 | 14 | |||||
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BlogMyData Resource Report Resource Website |
BlogMyData (RRID:SCR_008697) | software application, software resource, software development tool, blog, documentation generation software, data or information resource, narrative resource | Software tool for data sharing, incorporating blogs and spatial registration of data. Mainly used in geological data sets. A Virtual Research Environment (VRE) aims to combine the capabilities of two existing technologies that have already seen wide adoption among scientists: - The Godiva2 data visualization system provides a means for scientists to browse interactively in a ''Google Maps-like'' fashion through large environmental datasets, including numerical model outputs and high-resolution satellite imagery, using only a web browser. - The LabBlog is a web-based blogging tool specifically designed for the practising scientist to record, disseminate and evaluate their research. The Blog can also be used as a collaboration tool that allows secure discussion between colleagues. Although initially designed for the use of laboratory chemists, the LabBlog is being adapted in this project to meet the needs of environmental scientists. The BlogMyData VRE will allow scientists to explore data visually using Godiva2, then make comments about features in the data on a blog. Colleagues will discover these blog entries and offer further information, providing answers to research questions through comments. Through RSS and GeoRSS feeds, colleagues, investigators and other interested parties can be notified of research activity, and scientists can discover hitherto-unknown colleagues working with similar data in similar geographic regions. Sponsors: BlogMyData is a collaboration between the Reading e-Science Centre and the University of Southampton and is one of the JISC VRERI projects. | blog, technology, scientist, visualization, environmental, dataset, model, data | has parent organization: University of Southampton; Southampton; United Kingdom | nif-0000-37662 | SCR_008697 | BlogMyData | 2026-02-15 09:19:53 | 0 | |||||||||
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International Observatory on Neuro-Information Resource Report Resource Website 1+ mentions |
International Observatory on Neuro-Information (RRID:SCR_008690) | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The International Observatory on Neuro-Information is the central source of knowledge, research and data on all skills and issues for Neuroscience applied in Information Sciences. It is an initiative of the Documentation Sciences Foundation, from Spain, which aims to gather information, express opinions, prepare documents, make comparative research, support and promote policy-making, evaluate trends, and take other appropriate action relating to the Neuroscience and its application to the Information Sciences (Libraries, Archives, Documentation centers), and how the traditional knowledge of Information Sciences can bring expertise in data visualization and retrieval techniques, records management, quality assurance and usability in Neuroscience. The Observatory may work together, or in agreement with other national or international organizations pursuing similar or compatible aims. | observatory, neuroscience, research, knowledge, data, science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-37631 | SCR_008690 | Neuro-information | 2026-02-15 09:19:53 | 8 | |||||||||
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Brain Products Resource Report Resource Website 100+ mentions |
Brain Products (RRID:SCR_009443) | Brain Products GmbH | service resource, instrument manufacture, material service resource, production service resource | Commercial organization for hardware and software for neurophysiological research. Provides EEG and ERP amplifier systems, EEG recording caps, Data recording and analysis software, TMS Stimulator for combined EEG/TMS coregistrations and more. | manufacture, instruments, hardware, software, neurophysiological, research, EEG, ERP, EEG/fMRI, BCI, amplifier, recording, cap, data, analysis, software, TMS, stimulator | is related to: BrainVision Analyzer | nlx_155587 | SCR_009443 | 2026-02-15 09:20:08 | 105 | |||||||||
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GENEPOP Resource Report Resource Website 1000+ mentions |
GENEPOP (RRID:SCR_009194) | Genepop | software application, data processing software, data analysis software, software resource | Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Population, differentation, genetic, data, analysis, Hardy Weinberg Equilibrium test, statistics, genotyping, disequilibrium, pair, loci, allele, frequency |
is listed by: Genetic Analysis Software is listed by: CRAN |
PMID:21585727 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154337 | https://kimura.univ-montp2.fr/~rousset/Genepop.htm https://cran.r-project.org/web/packages/genepop/index.html |
SCR_009194 | genepop'007 | 2026-02-15 09:19:39 | 2266 | |||||
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miRDeep Resource Report Resource Website 100+ mentions |
miRDeep (RRID:SCR_010829) | miRDeep2 | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. | miRNA, gene, animal, clade, analysis, sequence, RNA, data | is listed by: OMICtools | Helmholtz-Alliance on Systems Biology ; Helmholtz Association ; German Ministry of Education and Research ; Senate of Berlin ; China Scholarship Council ; Max Delbrück Centrum Systems Biology Network |
PMID:18392026 PMID:21911355 |
Free, Available for download, Freely available | OMICS_00373 | https://github.com/rajewsky-lab/mirdeep2 | SCR_010829 | 2026-02-15 09:20:21 | 163 | |||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 500+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | portal, ontology, database, service resource, storage service resource, data repository, data or information resource, controlled vocabulary, topical portal, disease-related portal | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | NIH ; NIAID ; DAIT ; NIAID HHSN266200400076C; NIAID HHSN272201200028C |
PMID:24791905 | nlx_152691 | http://www.immport.org/immport-open/public/home/home http://www.immport.org/ |
http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-02-15 09:20:38 | 987 | |||
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eQTL Visualization Tool Resource Report Resource Website 1+ mentions |
eQTL Visualization Tool (RRID:SCR_013413) | software application, data visualization software, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics. | experiment, explore, expression, genome, genetic, genetical, cis, computational, data, database, genomic, grafical, interface, linkage, mine, pqtl type, p-value, repository, tissue, tissue type, trans, visualization, visualize | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10222 | SCR_013413 | eQTLexplorer | 2026-02-15 09:20:41 | 1 | |||||||||
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MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | data analysis service, software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canadian Institutes for Health Research ; Genome Alberta ; McGill University ; Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Research Chairs Program |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-02-15 09:21:19 | 10983 | |||||
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NeuroXM Brain Science Suite Resource Report Resource Website |
NeuroXM Brain Science Suite (RRID:SCR_016372) | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data. | semantic, data, graph, neuroscience, neuroanatomy, ontology, circuitry, pathway, multimodal, brain | Commercially available | SCR_016372 | Brain Science Suite, NeuroXM, NeuroXM Suite | 2026-02-15 09:21:38 | 0 | ||||||||||
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Research Data Management Platform Resource Report Resource Website 1+ mentions |
Research Data Management Platform (RRID:SCR_016268) | RDMP | data management software, software application, software resource, service resource, storage service resource, data repository, data or information resource, software toolkit | Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”. | metadata, reproducibility, anonymization, security, audit, clinical, dataset, translational, research, data, management, catalogue, health, informatics, linkage | has parent organization: University of Dundee; Scotland; United Kingdom | Medical Research Council (MRC) MR/M501633/1; Wellcome Trust WT086113; EU Horizon 2020 633983 |
Free, Available for download | https://hic.dundee.ac.uk/Installers/RDMP/Stable/ | SCR_016268 | 2026-02-15 09:21:36 | 2 | |||||||
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KiloSort Resource Report Resource Website 100+ mentions |
KiloSort (RRID:SCR_016422) | software application, data processing software, algorithm resource, software resource | Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings. | implement, integrated, template, matching, framework, detect, cluster, spike, multi, channel, electrophysiology, recording, data | is related to: MATLAB | Free, Available for download, Freely available | SCR_016422 | 2026-02-15 09:21:51 | 115 | ||||||||||
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Starbase V2.0 Resource Report Resource Website 500+ mentions |
Starbase V2.0 (RRID:SCR_016303) | web application, software resource | Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes. | visualize, analyze, discover, download, large, genomic, data, set, miRNA, RNA-RNA, protein-RNA, interaction, network, decoding, CLIP-Seq, Degradome-Seq | Ministry of Science and Technology of China ; National Basic Research Program No. 2011CB811300 |
PMID:24297251 | Free, Freely available, Available for download | SCR_016303 | 2026-02-15 09:21:04 | 819 | |||||||||
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Fractalis Resource Report Resource Website 1+ mentions |
Fractalis (RRID:SCR_016362) | software application, software library, data visualization software, data analysis service, software resource, data processing software, data access protocol, web service, service resource, production service resource, analysis service resource, software toolkit | Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis. | platform, independent, interactive, visual, analysis, biomedical, data, library | National Centre of Excellence in Research on Parkinson’s disease NCER13/BM/11264123; Luxembourg Ministry of Higher Education and Research |
Free, Available for download, Freely available | https://git-r3lab.uni.lu/Fractalis/fractalis/blob/master/README.md | SCR_016362 | 2026-02-15 09:21:51 | 1 | |||||||||
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lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | software application, data processing software, software resource, software toolkit, data analysis software | Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction. | personalized, medicine, metabolomics, data, classification, clustering, biomarker, prediction, algorithm, calculating, microarray, enrichment |
is listed by: OMICtools is related to: University of Hawaii; Hawaii; USA |
NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373; NICHD R01 HD084633 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-02-15 09:21:38 | 3 | |||||||
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The Pancreatic Beta-Cell Consortium Resource Report Resource Website 1+ mentions |
The Pancreatic Beta-Cell Consortium (RRID:SCR_016328) | PBC Consortium | portal, service resource, storage service resource, data repository, data or information resource, topical portal, disease-related portal | Portal to provide a repository for beta-cell data, to connect researchers from different backgrounds interested in contributing data, models and/or ideas for new insights into beta-cell biology. Used to understand beta-cell biology and diabetes through a cross-disciplinary approach for the assembly of spatiotemporal multi-scale whole cell models of human pancreatic beta-cells. | repository, pancreatic, Bcell, data, whole, cell, model, human, connect, contribute, model, idea, diabetes, integrate, approach, computation, design, effective, treatment, experiment, biology |
is related to: University of Southern California; Los Angeles; USA is related to: California Institute of Technology; Division of Biology is related to: University of California at Berkeley; Berkeley; USA is related to: Scripps Research Institute |
Diabetes | SCR_016328 | Pancreatic B Cell Consortium | 2026-02-15 09:21:51 | 4 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
