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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Seurat Resource Report Resource Website 10000+ mentions |
Seurat (RRID:SCR_016341) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is used by: scSidekick is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers works with: Connectome |
NHGRI 1DP2HG009623; NIMH 5R01MH071679; NSF |
PMID:29608179 | Free, Available for download, Freely available | https://satijalab.org/seurat/get_started.html | SCR_016341 | 2026-09-12 01:00:18 | 11480 | |||||||
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IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | alignment software, analysis service resource, data or information resource, data processing software, image analysis software, portal, production service resource, service resource, software application, software resource | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
CNRS ; GENCI ; MESR ; NHMRC ; Université Montpellier 2 ; France |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-09-12 01:00:21 | 15 | |||||
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Genie 2000 Basic Resource Report Resource Website 1+ mentions |
Genie 2000 Basic (RRID:SCR_021933) | data acquisition software, data analysis software, data processing software, software application, software resource | Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data. | Data acquisition, display, analysis, gamma and alpha spectrometry data | Restricted | SCR_021933 | Genie 2000 Basic Spectroscopy Software, Marion Technologies Genie 2000 Basic Spectroscopy Software, Marion Technologies Genie 2000 Basic | 2026-09-12 01:00:03 | 3 | ||||||||||
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Computational Biology at ORNL Resource Report Resource Website |
Computational Biology at ORNL (RRID:SCR_005710) | Computational Biology at ORNL | analysis service resource, data analysis service, production service resource, service resource | We are the Computational Biology and Bioinformatics Group of the Biosciences Division of Oak Ridge National Laboratory. We conduct genetics research and system development in genomic sequencing, computational genome analysis, and computational protein structure analysis. We provide bioinformatics and analytic services and resources to collaborators, predict prospective gene and protein models for analysis, provide user services for the general community, including computer-annotated genomes in Genome Channel. Our collaborators include the Joint Genome Institute, ORNL''s Computer Science and Mathematics Division, the Tennessee Mouse Genome Consortium, the Joint Institute for Biological Sciences, and ORNL''s Genome Science and Technology Graduate Program. | genetics, research, system development, genomic sequencing, computation, genome analysis, protein structure, analysis, gene, protein, gene annotation, annotation, genome | has parent organization: Oak Ridge National Laboratory | nlx_149161 | SCR_005710 | Computational Biology at Oak Ridge National Laboratory, Computational Biology and Bioinformatics Group at ORNL, Computational Biology Bioinformatics Group at ORNL | 2026-09-12 01:01:39 | 0 | ||||||||
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Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | Expression Profiler at the EBI | 2026-09-12 01:01:39 | 6 | ||||
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FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products Resource Report Resource Website |
FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products (RRID:SCR_005738) | FuSSiMeG | analysis service resource, data analysis service, production service resource, service resource | FuSSiMeG is being discontinued, may not be working properly. Please use our new tool ProteinOn. Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) provides a functional similarity measure between two proteins using the semantic similarity between the GO terms annotated with the proteins. Platform: Online tool | protein, similarity, gene ontology, gene, ontology, statistical analysis, term enrichment, semantic similarity, analysis, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: ProteInOn has parent organization: University of Lisbon; Lisbon; Portugal |
Free for academic use | nlx_149198 | SCR_005738 | Functional Semantic Similarity Measure between Gene-Products, Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) | 2026-09-12 01:01:39 | 0 | |||||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | analysis service resource, data analysis service, production service resource, service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | Lists2Networks: Integrated analysis of gene/protein lists | 2026-09-12 01:01:42 | 3 | |||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 500+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | analysis service resource, data analysis service, production service resource, service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-09-12 01:01:44 | 524 | |||||
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Bamboo DiRT Resource Report Resource Website 1+ mentions |
Bamboo DiRT (RRID:SCR_002556) | Bamboo DiRT | data or information resource, database | Registry of digital research tools for scholarly use that makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mindmapping software., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analysis, registry | is listed by: FORCE11 | Andrew W. Mellon Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156034 | http://www.force11.org/node/4756 | SCR_002556 | Bamboo Dirt registry of digital research tools for scholarly use, Bamboo Digital Research Tools | 2026-09-12 01:01:26 | 1 | |||||
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VIPERdb Resource Report Resource Website 50+ mentions |
VIPERdb (RRID:SCR_002853) | data or information resource, database | Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | exploration, analysis, capsid, computational, convention, database, icosahedral, structural, structure, system, virus, visual, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Scripps Research Institute |
PMID:33313778 PMID:30265627 |
Free, Freely available | nif-0000-25311, r3d100012362, nif-0000-03630, biotools:viperdb, SCR_007970 | https://bio.tools/viperdb, https://doi.org/10.17616/R3HT0Q | SCR_002853 | Virus Particle ExploreR | 2026-09-12 01:01:26 | 59 | ||||||
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SHEsis: Analysis Tools For Random Samples Resource Report Resource Website 50+ mentions |
SHEsis: Analysis Tools For Random Samples (RRID:SCR_002958) | SHEsis | analysis service resource, data analysis service, production service resource, service resource | A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. | analysis, disequilibrium, haplotype, genetic, association, polymorphism, locus, linkage disequilibrium | has parent organization: Shanghai Jiao Tong University; Shanghai; China | Major State Basic Research Development program of China ; National High Technology Research and Development Program of China |
PMID:19290020 PMID:15740637 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30105 | http://analysis.bio-x.cn/myAnalysis.php | SCR_002958 | 2026-09-12 01:01:27 | 82 | |||||
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SGD Resource Report Resource Website 1000+ mentions |
SGD (RRID:SCR_004694) | SGD, SGD LOCUS, SGD REF | data or information resource, database | A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available. | database, yeast, pathway, analysis, gene, nomenclature, predicted sequence, fungi, functional relationship, protein structure, bio.tools, FASEB list |
uses: InterMOD is used by: NIF Data Federation is used by: PhenoGO is listed by: re3data.org is listed by: OMICtools is listed by: InterMOD is listed by: bio.tools is listed by: Debian is affiliated with: InterMOD is related to: AmiGO is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: HomoloGene is related to: TXTGate is related to: PhenoGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford University; Stanford; California is parent organization of: Ascomycete Phenotype Ontology is parent organization of: SGD Gene Ontology Slim Mapper is organization facet of: Alliance of Genome Resources |
NHGRI 5P41HG001315-11; NHGRI 5P41HG002273-05; NHGRI 5U41HG001315-18; NHGRI 2U41HG002273-13; NHGRI 5R01HG004834-04 |
PMID:24265222 PMID:12519985 PMID:9399804 |
Free for academic use, The community can contribute to this resource, Non-commercial | nif-0000-03456, biotools:sgd, r3d100010419, OMICS_01661 | https://bio.tools/sgd, https://doi.org/10.17616/R3N313 | http://genome-www.stanford.edu/Saccharomyces/ | SCR_004694 | SGD LOCUS, Saccharomyces Genome Database, SGD REF | 2026-09-12 01:01:33 | 1950 | |||
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The Guardian: Science Resource Report Resource Website |
The Guardian: Science (RRID:SCR_005166) | Guardian: Science | blog, data or information resource, narrative resource | Latest science news, comment, analysis and features from guardian.co.uk, the world''s leading liberal voice. | science, news, comment, analysis, space, medicine, genetics, medical research |
is used by: NIF Data Federation is used by: Integrated Blogs |
nlx_144198 | SCR_005166 | 2026-09-12 01:01:35 | 0 | |||||||||
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Scientific American Observations Resource Report Resource Website |
Scientific American Observations (RRID:SCR_005195) | SA Observations | blog, data or information resource, narrative resource | From the editors and reporters of Scientific American, this blog delivers commentary, opinion and analysis on the latest developments in science and technology and their influence on society and policy. From reasoned arguments and cultural critiques to personal and skeptical takes on interesting science news, you''ll find a wide range of scientifically relevant insights here. | commentary, opinion, analysis, science, technology, society, policy |
is used by: NIF Data Federation is used by: Integrated Blogs has parent organization: Scientific American |
nlx_144201 | SCR_005195 | Scientific American - Observations | 2026-09-12 01:01:36 | 0 | ||||||||
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University of Salerno Laboratory of Molecular Medicine and Genomics Resource Report Resource Website |
University of Salerno Laboratory of Molecular Medicine and Genomics (RRID:SCR_011047) | UNISA LMMGe, UNISA, LMMGe, UNISA Laboratory of Molecular Medicine and Genomics, Laboratory of Molecular Medicine and Genomics | access service resource, core facility, service resource | Core equipped for structural and functional studies of genomes, includes equipment for next generation sequencing applications (Illumina HiSeq 1500, GAIIx and MiSeq, Life Technologies Ion Torrent PGM), RNA and microRNA expression profiling, array-based DNA methylation analyses and SNP genotyping (Illumina HiScan and Agilent High Resolution microarray scanners), informatics and bioinformatics (a server farm for genomics data computation and a high capacity data storage unit), fluorescence and confocal microscopy, long-term sample storage, cell culture, including a facility for generation and handling of viral vectors for gene transfer and gene therapy, access to a small animal facility for ''in vivo'' experimentations. Trained biotechnologists, molecular biologists and bioinformaticians handle all aspects related to experimental design, technical implementation and data analysis and storage. | genomes, sequencing, implementation, analysis, genotyping, cell culture, |
is listed by: ScienceExchange has parent organization: University of Salerno; Salerno; Italy |
Available to external user | SciEx_9722 | http://www.scienceexchange.com/facilities/laboratory-of-molecular-medicine-and-genomics | SCR_011047 | Laboratory of Molecular Medicine and Genomics, University of Salerno, UNISA, LMMGe | 2026-09-12 01:03:32 | 0 | ||||||
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Georgia Genomics and Bioinformatics Core at the University of Georgia Resource Report Resource Website 50+ mentions |
Georgia Genomics and Bioinformatics Core at the University of Georgia (RRID:SCR_010994) | GGBC | access service resource, core facility, service resource, training service resource | Core laboratory for nucleic acid sequencing and bioinformatics. Used for research support, education, and training. Services include genomic techniques and applications, sequencing technologies, and bioinformatics analyses, writting letters of support for grant applications submitted to funding agencies. GGBC operates multiple platforms for short-, long-, and single-molecule sequencing reads (i.e., Illumina MiSeq and NextSeq, PacBio Sequel, and Oxford Nanopore MinIon). | nucleic, acid, sequencing, labs, analysis, equipment, genomic, technique, analysis, grant, application |
is listed by: ScienceExchange is related to: University of Georgia Labs and Facilities has parent organization: University of Georgia; Georgia; USA |
SciEx_9234 | http://www.scienceexchange.com/facilities/georgia-genomics-facility-uga, http://www.scienceexchange.com/facilities/georgia-genomics-facility-uga | SCR_010994 | Georgia Genomics & Bioinformatics Core, Georgia Genomics and Bioinformatics Core at UGA, University of Georgia Genomics Facility, Georgia Genomics and Bioinformatics Core | 2026-09-12 01:03:31 | 75 | |||||||
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University of Southern California School of Pharmacy Translational Research Laboratory Resource Report Resource Website |
University of Southern California School of Pharmacy Translational Research Laboratory (RRID:SCR_012253) | USC, School of Pharmacy, TRLab, Translational Research Lab, University of Southern California, School of Pharmacy | access service resource, core facility, service resource | Core is equipped with a wide variety of technologically advanced instruments essential for cutting edge biomedical discovery and therapeutic development research. TRLab is composed of two major units. The Computational Bioinformatics Unit houses graphic workstations and modeling programs that enable in silico virtual screening and rational drug design applications. The Therapeutic Screening Unit houses a number of specialized instruments that enable a broad range of automated and multiplexed biological analyses in a throughput manner. The core mission of the TRLab has been to provide investigators with a state-of-the-art technological platform and technical expertise to advance translational research endeavors in the School of Pharmacy and at USC. | immunobiology, Molecular biology, analysis, imaging, |
is listed by: ScienceExchange has parent organization: University of Southern California; Los Angeles; USA |
Available to external user | SciEx_11044 | http://www.scienceexchange.com/facilities/the-translational-research-laboratory | SCR_012253 | USC, Translational Research Lab, Translational Research Laboratory, TRLab, University of Southern California, School of Pharmacy | 2026-09-12 01:03:39 | 0 | ||||||
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University of Southern California Epigenome Center Data Production Facility Resource Report Resource Website |
University of Southern California Epigenome Center Data Production Facility (RRID:SCR_012476) | USC Epigenome Center, | access service resource, core facility, service resource | Core conducts genome-scale epigenetic and genetic data production and analysis, technology development, and epigenomic and population-based genomic research. | genome-scale epigenetic, genetic data production, analysis, technology development, epigenomic, population-based genomic research |
is listed by: ScienceExchange is related to: University of Southern California Labs and Facilities has parent organization: University of Southern California; Los Angeles; USA |
Available to external user | SciEx_206 | SCR_012476 | University of Southern California Epigenome Center Data Production Facility | 2026-09-12 01:03:42 | 0 | |||||||
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Vancouver Prostate Centre Laboratory for Advanced Genome Analysis Resource Report Resource Website 1+ mentions |
Vancouver Prostate Centre Laboratory for Advanced Genome Analysis (RRID:SCR_012394) | VPC LAGA, LAGA | access service resource, core facility, service resource | Core offers sequencing and microarray services, solutions for the profiling of FFPE tissues, and complete, project-tailored downstream bioinformatics analysis. The core's structure enables the management of research projects from experimental design to analysis and interpretation of data as well as support for grant applications and publications. The LAGA provides open fee-for-service access as a core facility (intra-institutional services to its researchers) and as regional, national and international facility (inter-institutional services). | Microarray, Profiling of FFPE, Analysis |
is listed by: ScienceExchange is related to: Vancouver Prostate Centre Labs and Facilities has parent organization: University of British Columbia; British Columbia; Canada |
Available to external user | SciEx_13 | https://www.prostatecentre.com/our-research/core-facilities/LAGA | https://www.scienceexchange.com/labs/laboratory-for-advanced-genome-analysis | SCR_012394 | , Laboratory for Advanced Genome Analysis, PC-TRiADD, VPC | 2026-09-12 01:03:41 | 1 | |||||
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jMORP Resource Report Resource Website 100+ mentions |
jMORP (RRID:SCR_024755) | data or information resource, database | Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies. | Japanese population, multi omics reference panel, plasma metabolome and proteome analyses, metabolome, genome, transcriptome, metagenome, datasets, samples, analysis, | Japan Agency for Medical Research and Development | DOI:10.1093/nar/gkad978 | Restricted | SCR_024755 | 2026-09-12 01:04:30 | 109 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
