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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GoatMap Database Resource Report Resource Website |
GoatMap Database (RRID:SCR_008144) | data repository, storage service resource, portal, data or information resource, service resource, topical portal, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This website contains information about the mapping of the caprine genome. It contains loci list, phenes list, cartography, gene list, and other sequence information about goats. This website contains 731 loci, 271 genes, and 1909 homologue loci on 112 species. It also allows users to summit their own data for Goatmap. ARK-Genomics is not-for-profit and has collaborators from all over the world with an interest in farm animal genomics and genetics. ARK-Genomics was initially set up in 2000 with a grant awarded from the BBSRC IGF (Investigating Gene Function) initiative and from core resources of the Roslin Institute to provide a laboratory for automated analysis of gene expression using state-of-the-art genomic facilities. Since then, ARK-Genomics has expanded considerably, building up considerable expertise and resources. | farm, gene, animal, caprine, cartography, genome, genomic, goat, homologue, locus, map, mapping, phene, sequence | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20978 | SCR_008144 | GoatMap | 2026-02-14 02:01:34 | 0 | |||||||||
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GeneNetWorks Resource Report Resource Website 1+ mentions |
GeneNetWorks (RRID:SCR_008034) | data visualization software, data processing software, data acquisition software, data or information resource, data analysis software, software application, software resource, database | GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses. | experimental, expression, gene, gene regulation, genetic, analysis, data, dna, graphical, molecular, navigation, network, program, protein, rna, software, system | nif-0000-10232 | SCR_008034 | GNW | 2026-02-14 02:01:32 | 1 | ||||||||||
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Gene Regulation Databases Resource Report Resource Website 100+ mentions |
Gene Regulation Databases (RRID:SCR_008033) | Gene Regulation Public Databases | data or information resource, portal, topical portal | In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes. | element, eukaryote, eukaryotic, expression, functionally, gene, genome, alignment, bind, binding site, cell, chromatin, collaborative, component, coupling, disease, dna, domain, human, matrix, molecular weight, molecule, mononucleotide, network, nucleotide, nucleus, pathological, protein, region, regulated, regulatory, scientific research, sequence, signaling, signal pathway, transcription factor, molecular neuroanatomy resource |
lists: TRANSFAC has parent organization: BIOBASE Corporation |
BIOBASE | nif-0000-10230 | SCR_008033 | gene-regulation.com: Public Databases for Academic and Non-profit Organizations | 2026-02-14 02:01:35 | 130 | |||||||
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HPV Sequence Database Resource Report Resource Website 1+ mentions |
HPV Sequence Database (RRID:SCR_008154) | data or information resource, portal, database, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 23, 2016. The Human Papillomaviruses Database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. It includes molecular biologists, sequence analysts, computer technicians, post-docs and graduate research assistants. This Web site has two main branches. The first contains our four annual data books of papillomavirus information, called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. and the second contains papillomavirus genetic sequence data. There is also a New Items location where we store the latest changes to the database or any other current news of interest. Besides the compendium, we also provide genetic sequence information for papilloma viruses and related cellular proteins. Each year they publish a compendium of papillomavirus information called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. which can now be downloaded from this Web site. | gene, genetic, alignment, amino acid, biologist, cellular protein, genome, human, molecular, papilloma, papillomavirus, phylogenetic, sequence, virus | has parent organization: Los Alamos National Laboratory | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21000 | http://www.stdgen.lanl.gov/ | SCR_008154 | HPVSD | 2026-02-14 02:01:34 | 4 | |||||||
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Genomatix Software: Understanding Gene Regulation Resource Report Resource Website 500+ mentions |
Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) | data processing software, short course material, portal, data or information resource, data analysis software, software application, software resource, narrative resource, training material, topical portal, database | Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc. | effect, expression, functional, gene, genome, alignment, analysis, annotation, biological, cascade, cell, data, dna, in-silico analysis, mechanism, metabolic pathway, microarray, mining, molecular, network, pathway, promoter, protein, region, regulation, scientific, sequence, signaling, software, stimulus, systems biology, technology, text mining, transcription, FASEB list | has parent organization: Genomatix Solutions | nif-0000-10236 | http://www.genomatix.de/products/index.html | SCR_008036 | Genomatix | 2026-02-14 02:01:37 | 868 | ||||||||
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AraCyc Resource Report Resource Website 50+ mentions |
AraCyc (RRID:SCR_008109) | data repository, storage service resource, data or information resource, service resource, database | Curated species-specific database present at the Plant Metabolic Network. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways. | enzyme, gene, arabidopsis thaliana, biochemical, pathway, reaction, metabolism, metabolic pathway, data set, data analysis service, web service, FASEB list |
is used by: Arabidopsis Reactome is listed by: 3DVC has parent organization: Plant Metabolic Network |
NSF | PMID:12805578 PMID:15888675 |
The community can contribute to this resource | nif-0000-20811 | http://www.arabidopsis.org/biocyc/index.jsp http://www.plantcyc.org |
SCR_008109 | Arabidopsis enzymes and biochemical pathways database | 2026-02-14 02:01:29 | 69 | |||||
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Department of Psychiatry, Turner Laboratory Resource Report Resource Website |
Department of Psychiatry, Turner Laboratory (RRID:SCR_008067) | Turner Lab | laboratory portal, data or information resource, organization portal, portal | Dr. Eric Turner''s laboratory studies the mechanisms underlying the development of the nervous system. The vertebrate brain is comprised of a tremendous variety of neurons, each class exhibiting a unique phenotype characterized by the expression of specific neurotransmitter receptors, ion channels, patterns of axonal growth, and synapse formation. The research we conduct focuses on the critical role transcription factors play in the specification of neuronal cell type during development. We are particularly interested in transcription factors of the homeodomain family that bind to DNA and in doing so activate or repress gene expression. One area of study is the role of POU-domain transciption factor Brn3a in axon growth and survival. The primary research areas are: * Neuronal cell fate determination: The expression of regulatory genes is manipulated in living chick embryos using microsurgery and electroporation and the effects on neural marker genes studied. * Molecular mechanisms of gene regulation: Target DNA binding sites of neural transcription factors are biochemically characterized and findings coordinated with sequence data from the mouse and human genomes. * Targeted misexpression of regulatory genes: Transgenic and knockout mouse technology is used to misexpress genes of interest, and the effects on neural marker genes, axonal growth, and cell survival studied. * Global analysis of neural gene expression: Micro-arrays (GeneChips) are employed in conjunction with other areas of study to understand the coordinated regulation of gene expression in the nervous system. Dr. Turner is a member of the University of California, San Diego''s Graduate Program in Neuroscience and Biomedical Sciences Program and accepts students from these two programs. Interesting rotation projects are available using methods ranging from biochemistry and molecular biology to embryology. Additionally, Dr. Turner is also the Director of this NIMH-funded training program for research-oriented psychiatrists, psychologists, and basic neuroscientists working in areas relevant to psychiatry. Typically Fellows spend two years in the program, during which they develop a research project under the close supervision of one of the highly productive members of the UCSD Department of Psychiatry, or another investigator in the La Jolla (UCSD/Salk/Scripps) research community. | electroporation, embryo, embryology, expression, gene, axon, biochemistry, biomedical science, cell, c hick, development, dna, dna binding site, homeodomain, human, knockout technology, microarray, microsurgery, misexpression, molecular biology, molecular mechanism, mouse, nervous system, neural gene, neural marker gene, neural transcription factor, neuronal cell, neuroscience, neuroscientist, psychiatrist, psychologist, regulation, regulatory gene, transcription factor, transgenic technology | has parent organization: University of California at San Diego Department of Psychiatry | nif-0000-10507 | SCR_008067 | UCSD Turner Laboratory, UCSD Psychiatry (Turner''s Lab), Turner Laboratory, Turner Laboratory Developmental Neurobiology Research | 2026-02-14 02:01:37 | 0 | ||||||||
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GeneWindow Resource Report Resource Website 1+ mentions |
GeneWindow (RRID:SCR_008183) | data analysis software, software resource, data processing software, software application | Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible | gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set |
is listed by: 3DVC has parent organization: National Cancer Institute |
nif-0000-21173 | SCR_008183 | GeneWindow | 2026-02-14 02:01:37 | 1 | |||||||||
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RIKEN Omics Science Center Resource Report Resource Website |
RIKEN Omics Science Center (RRID:SCR_008241) | portal, data or information resource, research forum portal, disease-related portal, topical portal | Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level. | expression, gene, genome, human, intracellular, life, living, model organisms and comparative genomics databases, molecule, omics, organism, pathway, protein, proteome, science, sequence, technology, transcriptome | is parent organization of: FANTOM DB | RIKEN Yokohama Institute Yokohama Research Promotion Division of Japan | nif-0000-21361 | SCR_008241 | RIKEN OSC | 2026-02-14 02:01:39 | 0 | ||||||||
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repairGenes Resource Report Resource Website 1+ mentions |
repairGenes (RRID:SCR_008240) | data or information resource, portal, topical portal | The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system. | gene, gene-, biological, dna, or disease- specific databases, organism, repair, specie, system- | has parent organization: University of Oslo; Oslo; Norway | nif-0000-21359 | SCR_008240 | repairGenes | 2026-02-14 02:01:35 | 1 | |||||||||
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Abgent Resource Report Resource Website 50+ mentions |
Abgent (RRID:SCR_008393) | commercial organization | Antibody supplier. | antibody, peptide, synthesis, protein, primary antibody, reagent, peptide synthesis, cell signaling, post-translational modification, stem cell, neuronal development, neurodegenerative disease, gene regulation, development, autophagy, apoptosis, stem cell, phosphorylation, cell function, gene, regulation, research, library, human, kinome, cdna clone, rnai, tissue, cell | is listed by: ScienceExchange | nif-0000-30051, SciEx_4353 | https://www.abcepta.com/ | SCR_008393 | Abgent Antibodies and Peptides, Abcepta | 2026-02-14 02:01:33 | 67 | ||||||||
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Nature Supplements: Collections archive Resource Report Resource Website |
Nature Supplements: Collections archive (RRID:SCR_008337) | data or information resource, narrative resource, portal, topical portal | This website provides summary collections written for a broad audience highlighting some of the significant advances in a particular field. These are not scientific articles although they may reference scientific work. Sponsors: This resource is supported by Nature.com | drug, energy, gene, gene targeting, aids, animal, biogenesis, cancer, cell, disease, genomics, health, hiv, human immunodeficiency virus, malaria, metagenomics, microrna, mrna, nanotechnology, neuropathic, pain, rnai, rna plant, therapy, vaccine | nif-0000-24926 | SCR_008337 | Nature Collections Supplements | 2026-02-14 02:01:41 | 0 | ||||||||||
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Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | sequence analysis software, data processing software, web application, data analysis software, software application, software resource | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-02-14 02:01:38 | 3542 | |||||
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GeneTraffic Resource Report Resource Website 10+ mentions |
GeneTraffic (RRID:SCR_008651) | data processing software, data management software, data analysis software, software application, software resource | GeneTraffic is a web-based microarray data analysis and management software developed by Iobion Informatics that allows users to log onto a server, upload their microarray data and perform analysis and project management remotely. GeneTraffic was made by Iobion Informatics (now under Stratagene) and can be accessed thorough Internet Explorer 6.0 or greater on Windows XP. | gene, data, management, microarray, software | nif-0000-33028 | SCR_008651 | 2026-02-14 02:01:38 | 24 | |||||||||||
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DataAssist Resource Report Resource Website 100+ mentions |
DataAssist (RRID:SCR_014969) | data visualization software, data processing software, data analysis software, software application, software resource | Data analysis tool that utilizes the Comparative CT (ddCT) method to rapidly and accurately quantitate relative gene expression across a large number of genes and samples. Raw input from plates or arrays can be analyzed according to user-determined settings. | ddCT, QC analysis, comparative ct, gene expression, data analysis, gene, plot | has parent organization: Thermo Fisher Scientific | Free, Available for download, Account required | SCR_014969 | DataAssist Software | 2026-02-14 02:03:00 | 454 | |||||||||
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BrainStars Resource Report Resource Website 10+ mentions |
BrainStars (RRID:SCR_005810) | B* | web service, data or information resource, data access protocol, software resource, database | BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API. | mouse, brain, adult, expression profile, affymetrix genechip mouse genome 430 2.0 array, rna, central nervous system, gene expression, gene |
is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science has parent organization: RIKEN has parent organization: Kindai University School of Medicine; Osaka; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21858037 | BrainStars data, Images and texts (excluding ABA data and images) are licensed under a Creative Commons Attribution 2.1 Japan License. | nlx_149301 | SCR_005810 | BrainStars Database, BrainStars (B*) | 2026-02-14 02:01:01 | 14 | |||||
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GARBAN Resource Report Resource Website |
GARBAN (RRID:SCR_005778) | GARBAN | data analysis service, analysis service resource, production service resource, source code, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. GARBAN is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban (at) ceit.es. Platform: Online tool | cdna microarray, proteomics, cdna, microarray, statistical analysis, gene, est, protein, genomic, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
PMID:14594726 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149247 | http://garban.tecnun.es | SCR_005778 | Genomic Analysis and Rapid Biological ANnotation, University of Navarra; Pamplona; Spain | 2026-02-14 02:01:10 | 0 | |||||
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FunCluster Resource Report Resource Website 1+ mentions |
FunCluster (RRID:SCR_005774) | FunCluster | data analysis software, software resource, data processing software, software application | FunCluster is a genomic data analysis algorithm which performs functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis aims to detect co-regulated biological processes through a specially designed clustering procedure involving biological annotations and gene expression data. FunCluster''''s functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo Sapiens, Mus Musculus and Saccharomyces Cerevisiae. FunCluster is provided as a standalone R package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix). Download it from the FunCluster website, or from the worldwide mirrors of CRAN. FunCluster is provided freely under the GNU General Public License 2.0. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genomic, gene, functional analysis, gene expression, cdna microarray, cdna, microarray, function, cluster, annotation, biological process, statistical analysis, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Cordelier Research Center |
PMID:17007070 PMID:16506959 PMID:16046292 |
Free for academic use, GNU General Public License, v2 | nlx_149242, biotools:funcluster | https://bio.tools/funcluster | SCR_005774 | FunCluster R Package, FunCluster Algorithm | 2026-02-14 02:00:58 | 2 | |||||
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GREAT: Genomic Regions Enrichment of Annotations Tool Resource Report Resource Website 50+ mentions |
GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) | GREAT | data analysis service, analysis service resource, production service resource, source code, service resource, software resource | Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool | term enrichment, cis-regulatory region, function, gene, genomic, annotation, ontology, chromatin immunoprecipitation, sequencing, chip-seq, comparative genomics, transcription factor binding |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: PRISM (Stanford database) is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
Bio-X ; Howard Hughes Medical Institute ; Stanford University; California; USA ; Packard ; Searle Scholar ; Microsoft Research ; Alfred P. Sloan Foundation ; Edward Mallinckrodt Jr. Foundation ; NIH ; Human Frontier Science Program fellowship LT000896/2009-l; NICHD 1R01HD059862; NHGRI R01HG005058; NSF CCF-0939370; DFG Hi 1423/2-1 |
PMID:20436461 PMID:23814184 |
Free for academic use, Acknowledgement requested | nlx_149295, OMICS_00635 | SCR_005807 | Genomic Regions Enrichment of Annotations Tool (GREAT), Genomic Regions Enrichment of Annotations Tool | 2026-02-14 02:01:10 | 82 | |||||
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GOHyperGAll Resource Report Resource Website 1+ mentions |
GOHyperGAll (RRID:SCR_005766) | GOHyperGAll | data analysis software, software resource, data processing software, software application | To test a sample population of genes for overrepresentation of GO terms, the R/BioC function GOHyperGAll computes for all GO nodes a hypergeometric distribution test and returns the corresponding p-values. A subsequent filter function performs a GO Slim analysis using default or custom GO Slim categories. Basic knowledge about R and BioConductor is required for using this tool. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene ontology, annotation, statistical analysis, slimmer-type tool |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of California at Riverside; California; USA |
PMID:18354039 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149267 | SCR_005766 | 2026-02-14 02:00:58 | 4 |
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If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
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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.
