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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BLASTX Resource Report Resource Website 10000+ mentions |
BLASTX (RRID:SCR_001653) | BLASTX | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level. | protein, translated nucleotide, blast, nucleotide, expressed sequence tag, sequence, genome, wgs, peptide, alignment, dna |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
PMID:28902395 PMID:8485583 |
Free, Freely Available | nlx_153933, OMICS_00992 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001653 | Translated BLAST, Translated BLAST: blastx | 2026-09-19 12:49:44 | 10411 | |||||
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APHIDBASE Resource Report Resource Website 50+ mentions |
APHIDBASE (RRID:SCR_001765) | AphidBase | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Aphid genome database. Facilitates community annotation of pea aphid genome by International Aphid Genomics Consortium (IAGC). It aims to store recently acquired genomic resources on aphids and compare them to other insect resources as functional annotation tools. AphidBase Information System designed to organize and distribute genomic data and annotations for large international community was constructed using open source software tools from Generic Model Organism Database (GMOD). | aphid, aphid gene sequence, aphid genome, aphid nervous system, genome, blast, annotate, annotation, est, function, FASEB list | has parent organization: INRA Rennes | ANR Exdisum ; ANR Genoplante ; Rennes Metropole |
PMID:20482635 PMID:17237053 |
Free, Freely available | nif-0000-02554 | http://w3.rennes.inra.fr/AphidBase | http://www.aphidbase.com/ | SCR_001765 | The Aphid Genome Database, Aphid Genome Database | 2026-09-19 12:49:48 | 69 | |||
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Diabetes Disease Portal Resource Report Resource Website |
Diabetes Disease Portal (RRID:SCR_001660) | Diabetes Disease Portal | data or information resource, data set, disease-related portal, portal, topical portal | An integrated resource for information on genes, QTLs and strains associated with diabetes. The portal provides easy acces to data related to both Type 1 and Type 2 Diabetes and Diabetes-related Obesity and Hypertension, as well as information on Diabetic Complications. View the results for all the included diabetes-related disease states or choose a disease category to get a pull-down list of diseases. A single click on a disease will provide a list of related genes, QTLs, and strains as well as a genome wide view of these via the GViewer tool. A link from GViewer to GBrowse shows the genes and QTLs within their genomic context. Additional pages for Phenotypes, Pathways and Biological Processes provide one-click access to data related to diabetes. Tools, Related Links and Rat Strain Models pages link to additional resources of interest to diabetes researchers. | gene, quantitative trait locus, strain, diabetic complication, genome, gviewer, genomic, phenotype, pathway, biological process, chromosome, visualization, molecular function, cellular component, synteny |
is related to: NIDDK Information Network (dkNET) is related to: Gene Ontology has parent organization: Rat Genome Database (RGD) |
Type 1 diabetes, Type 2 diabetes, Diabetes, Obesity, Hyperlipidemia, Metaboic disease, Hypertension | Free, Freely Available | nlx_153942 | http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=diabetes | SCR_001660 | 2026-09-19 12:49:44 | 0 | ||||||
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ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | data or information resource, data repository, database, service resource, storage service resource | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571, r3d100010666 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-09-19 12:49:48 | 53 | ||||
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TCAG Resource Report Resource Website 50+ mentions |
TCAG (RRID:SCR_001840) | TCAG | analysis service resource, biomaterial analysis service, biomaterial manufacture, data or information resource, database, material analysis service, material service resource, portal, production service resource, service resource, topical portal, training service resource | Service and training support for academic, government, and private sector scientists worldwide in genomics, including laboratory experimentation, statistical analysis, and comprehensive bioinformatics support, including large-scale genome comparisons, algorithm and tools development, and database curation, annotation and hosting. The Centre for Applied Genomics hosts a variety of databases related to ongoing supported projects: *Autism Chromosome Rearrangement Database *Cystic Fibrosis Mutation Database *The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database *Database of Genomic Variants *The Chromosome 7 Annotation Project *Human Genome Segmental Duplication Database *Non-Human Segmental Duplication Database Healthy control DNA samples from the Ontario Population Genomics Platform are available. The Biobanking and Databasing Facility provides DNA extraction from lymphoblasts, fibroblasts and other cell types, archiving of white cell pellets, preparation and immortalization of cell lines, and comprehensive databasing and tracking of samples and/or cell lines within the facility. | genomics, publication, link, bioinformatics, genome, research, microarray analysis, gene expression, genotyping, biobanking, statistical analysis, genetic analysis, cytogenomics, dna sequencing, dna synthesis, comparative genomic hybridization, karyotyping, fish mapping, human, mouse, gene expression, biobanking, dna, mutation, genomic variant, chromosome 7, FASEB list | is listed by: One Mind Biospecimen Bank Listing | Healthy control, Autism, Cystic fibrosis, Epilepsy, Polymorphism | Free, Freely available | nif-0000-12519 | SCR_001840 | Centre for Applied Genomics, The Centre for Applied Genomics | 2026-09-19 12:49:48 | 84 | ||||||
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Arabidopsis thaliana Genome Database Resource Report Resource Website 10+ mentions |
Arabidopsis thaliana Genome Database (RRID:SCR_001901) | AtGDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing. | expressed sequence tag, est sequence, contig, gene structure, genome, arabidopsis thaliana, cdna, plant database, blast, annotation | has parent organization: Iowa State University; Iowa; USA | NSF IOS-0606909; NSF DBI-0110254; NSF DBI-0321600 |
PMID:16219921 PMID:14681433 PMID:12805580 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02582 | SCR_001901 | Arabidopsis thaliana Genome DB | 2026-09-19 12:49:49 | 10 | |||||
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Aspergillus Genomes Resource Report Resource Website |
Aspergillus Genomes (RRID:SCR_001880) | Aspergillus Genomes | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A resource for viewing annotated genes arising from various Aspergillus sequencing and annotation projects, resulting from the merging of Central Aspergillus Data REpository (CADRE) and The Aspergillus Website, which took place in June 2008. The principal role of CADRE is to aid the Aspergillus research community by managing Aspergillus genome data and by providing visualization tools, ranging from relatively simple annotation displays to more complex data integration displays. In contrast, The Aspergillus Website provides a range of information to the medical community (i.e., clinicians, patients and scientists) regarding the genus Aspergillus and the diseases, such as Aspergillosis, that it can cause. CADRE has been implemented using the Ensembl v22 suite. This suite comprises: * a database schema, which has been devised for storing annotated eukaryotic genomes. The schema is implemented with the MySQL relational database management system. * several specialized programming modules for building interfaces (i.e., BioPerl and Ensembl API modules). * a series of programs (i.e., Perl CGI scripts using the API modules) for viewing genomic data within a web browser., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genome, eukaryotic genome, gene, gene annotation, aspergillosis, aspergillus, pathway, annotation, sequence, metabolic pathway, genomics, clinical, strain, dna, peptide, blast | Fungal Research Trust | PMID:19039001 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02577, r3d100011253 | https://doi.org/10.17616/R3005P | SCR_001880 | 2026-09-19 12:49:49 | 0 | ||||||
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DAVID Resource Report Resource Website 10000+ mentions |
DAVID (RRID:SCR_001881) | DAVID | data access protocol, data or information resource, database, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis. | functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualization, FASEB list |
is listed by: OMICtools is listed by: 3DVC is listed by: LabWorm is listed by: SoftCite is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG has parent organization: NCI-Frederick |
NCI ; NIAID NO1-CO-56000 |
PMID:19131956 PMID:12734009 PMID:35325185 PMID:22543366 PMID:17980028 PMID:17576678 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30408, OMICS_02220, nif-0000-10451, SCR_003033 | http://david.abcc.ncifcrf.gov/ | SCR_001881 | DAVID Bioinformatics Resources, Visualization and Integrated Discovery Bioinformatics Resources, Database for Annotation Visualization and Integrated Discovery, The Database for Annotation, The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources | 2026-09-19 12:49:49 | 20855 | ||||
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MouseCyc Resource Report Resource Website 10+ mentions |
MouseCyc (RRID:SCR_001791) | MouseCyc | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database. | energy production, biosynthesis, cell, cellular, degradation, detoxification, metabolism, mouse, physiological, enzymatic reaction, gene, disease, genome, metabolic pathway, pathway, compound, enzymatic reaction, protein, rna, reaction, blast, human, mammal, genetic, genomic |
is related to: Mouse Genome Informatics (MGI) is related to: Gene Ontology has parent organization: Jackson Laboratory |
NHGRI HG003622 | PMID:19682380 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10303 | SCR_001791 | MouseCyc database, Mouse Genome Informatics: MouseCyc database | 2026-09-19 12:49:48 | 10 | |||||
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Rat Resource and Research Center Resource Report Resource Website 100+ mentions |
Rat Resource and Research Center (RRID:SCR_002044) | NRRRC, RRRC, NCRR RRRC | biomaterial supply resource, cell repository, material resource, organism supplier | Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. | RIN, Resource Information Network, embryo, gamete, animal, drug, biomedical, cryopreserved, disease, genome, genotyping, germplasma, human, hybrid, inbred, infectious, molecular, mutant, nuclear, ovarian, pathogen, rat, research, tissue, rat model, embryonic stem cell, reagent, protocol, cell line, stem cell, strain, database, catalog, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: One Mind Biospecimen Bank Listing has parent organization: University of Missouri; Missouri; USA |
NCRR P40 RR016939; NIH Office of the Director P40 OD011062 |
Free | nif-0000-12085 | http://www.nrrrc.missouri.edu/ | SCR_002044 | National Rat Resource Research Center, National Center for Research Resources, Rat Resource & Research Center, Rat Resource and Research Center, Rat Resource Research Center, NCRR | 2026-09-19 12:49:52 | 230 | |||||
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Candida Genome Database Resource Report Resource Website 500+ mentions |
Candida Genome Database (RRID:SCR_002036) | CGD, CGD LOCUS, CGD REF | data or information resource, data repository, database, service resource, storage service resource | Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome. | protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: ASPGD is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
NIDCR DE015873 | PMID:19808938 | Free, Available for download, Freely available | biotools:cgd, nif-0000-02634, r3d100010617 | https://bio.tools/cgd | SCR_002036 | 2026-09-19 12:49:53 | 506 | |||||
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DMET-Analyzer Resource Report Resource Website 1+ mentions |
DMET-Analyzer (RRID:SCR_002030) | DMET-Analyzer | software resource | Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way. | drug, metabolism, enzyme, transporter, affymetrix, variation, genome, clinical, affymetrix dmet, single nucleotide polymorphism, annotation, analysis, pharmacogenomic, pathway |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23035929 | Free, Available for download, Freely available | OMICS_01920 | SCR_002030 | DMETANALYZER, DMETANALYZER - A tool for supporting pharmacogenomics data analysis | 2026-09-19 12:49:52 | 1 | ||||||
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CMHD - Centre for Modeling Human Disease Resource Report Resource Website 10+ mentions |
CMHD - Centre for Modeling Human Disease (RRID:SCR_006101) | CMHD | analysis service resource, biomaterial manufacture, data or information resource, database, material service resource, production service resource, service resource | Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges | mutant, mouse model, chemical mutagenesis, ethylnitrosourea, gene trap insertion, mutagenesis, genome-wide mutagenesis, mouse genome, genome, phenotype, heritability, expression pattern, sequence, image, neurobiology, behavior, embryonic stem cell, gene trapping, enu mutagenesis, human disease |
has parent organization: Toronto Centre for Phenogenomics is parent organization of: Centre for Modeling Human Disease Gene Trap Resource |
Human disease | CIHR ; Genome Canada |
Non-CMHD users are required to register and log in only if you wish to view images on our mouse models. | nlx_151636 | SCR_006101 | Centre for Modeling Human Disease | 2026-09-19 12:51:04 | 12 | |||||
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GWAS Central Resource Report Resource Website 100+ mentions |
GWAS Central (RRID:SCR_006170) | data or information resource, data repository, database, service resource, storage service resource | Publicly available database of summary level findings from genetic association studies in humans, including genome wide association studies (GWAS). Previously named HGBASE, HGVbase and HGVbaseG2P. | Human Genome Variation database of Genotype-to-Phenotype information, genetic association study, genotype, phenotype, gene, genome region, disease, frequency data, region, genome, marker, single nucleotide polymorphism, genetic variant, allele, genome wide association study, human genome, chromosome, genetics |
is listed by: re3data.org is related to: dbSNP has parent organization: University of Leicester; Leicester; United Kingdom |
European Union GEN2PHEN project ; GlaxoSmithKline ; University of Leicester; Leicester; United Kingdom |
PMID:18948288 | nlx_151672, nif-0000-02958, SCR_007709, r3d100010565 | http://www.hgvbaseg2p.org, https://doi.org/10.17616/R34G8W | SCR_006170 | Genome Wide Association Studies Central, Human Genome Variation database of Genotype to Phenotype information, HGVbaseG2P | 2026-09-19 12:51:05 | 114 | ||||||
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WashU Epigenome Browser Resource Report Resource Website 100+ mentions |
WashU Epigenome Browser (RRID:SCR_006208) | Human Epigenome Browser | data analysis software, data or information resource, data processing software, data set, software application, software resource, source code | Software tool for visualizing and interacting with whole-genome datasets. Browser hosts Human Epigenome Atlas data produced by Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. Developed and maintained by Epigenome Informatics Group at Washington University in St. Louis. | epigenomics, genome browser, visualization, clustering, genome, sequencing, next-generation sequencing, virus |
is listed by: OMICtools is related to: VizHub is related to: UCSC Genome Browser is related to: Human Epigenome Atlas has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Roadmap Epigenomics Project |
PMID:22127213 | Free, Freely available | OMICS_00629, nlx_151754 | http://epigenomegateway.wustl.edu/browser/ | SCR_006208 | WashU Epigenome Browser, WashU Genome Browser, Human Epigenome Browser at Washington University | 2026-09-19 12:51:06 | 184 | |||||
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InterSpecies Analysing Application using Containers Resource Report Resource Website 10+ mentions |
InterSpecies Analysing Application using Containers (RRID:SCR_006243) | ISAAC | analysis service resource, data analysis service, production service resource, service resource, software resource | Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups. | protein function, protein interaction, pathway, mirna, disease, drug, gene, genome, transcript, protein, regulation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Wurzburg; Bavaria; Germany |
PMID:24428905 | OMICS_02237 | SCR_006243 | ISAAC (Interspecies Analysing Application using Containers), ISAAC - InterSpecies Analysing Application using Containers, Interspecies Analysing Application using Containers - ISAAC | 2026-09-19 12:51:06 | 37 | |||||||
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modENCODE Resource Report Resource Website 100+ mentions |
modENCODE (RRID:SCR_006206) | modENCODE | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets. | epigenomics, epigenetics, genomics, functional element, model organism, genome, copy number variation, gene structure, genome sequence, histone modification, histone replacement, chromatin binding site, expression profiling, replication, transcription factor binding site, transcription factor, binding site, chromatin, rna, expression profiling, regulatory network, mrna, ncrna, dna replication, genotype |
is related to: ENCODE is related to: Encode |
NHGRI | PMID:19536255 | Public, With some restrictions on its use for 9 months following publication, Acknowledgement requested | nlx_151752 | SCR_006206 | NHGRI model organism ENCyclopedia Of DNA Elements, National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements, model organism ENCyclopedia Of DNA Elements | 2026-09-19 12:51:06 | 260 | |||||
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Spark Resource Report Resource Website 100+ mentions |
Spark (RRID:SCR_006207) | Spark | data analysis software, data processing software, data visualization 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 | 2026-09-19 12:51:06 | 417 | |||||
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Genomic Standards Consortium Resource Report Resource Website 10+ mentions |
Genomic Standards Consortium (RRID:SCR_006273) | GSC | data or information resource, international standard specification, knowledge environment, narrative resource, standard specification | An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community | genome, genomics, standards |
is listed by: OMICtools is related to: Minimum Information for Biological and Biomedical Investigations is related to: FAIRsharing is related to: Ontology for Biomedical Investigations is related to: OBO is related to: ISA Infrastructure for Managing Experimental Metadata is parent organization of: Gazetteer |
National Institute for Environmental eScience ; NERC NE/3521773/1 |
nlx_151884, OMICS_01780 | http://gensc.org/gc_wiki/index.php/Main_Page | SCR_006273 | 2026-09-19 12:51:07 | 32 | |||||||
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CGARS Resource Report Resource Website |
CGARS (RRID:SCR_006404) | CGARS | software resource | Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines. | genome, analysis |
is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Cancer | PMID:24413525 | GNU General Public License, v3 or later | OMICS_02210 | SCR_006404 | CGARS: Cancer Genome Analysis by Rank Sums, Cancer Genome Analysis by Rank Sums | 2026-09-19 12:51:10 | 0 |
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