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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRISPOR Resource Report Resource Website 1000+ mentions |
CRISPOR (RRID:SCR_015935) | web application, software resource | Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track. | rna, sg, sgrna, crispr, genome, off-target, prediction, accuracy, clone, cas9, coding, exon | is related to: UCSC Genome Browser | MRC 53658; NIH Office of the Director U42 OD011174; NHGRI U41 HG002371; NCI U54 HG007990; California Institute of Regenerative Medicine GC1R-06673C; Agence Nationale pour la Recherche ; Fondation pour la Recherche Médicale DEQ20140329544 |
PMID:27380939 | Free, Available for download | https://github.com/maximilianh/crisporWebsite | SCR_015935 | 2026-02-15 09:21:28 | 1320 | |||||||
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loadBAM2ge_db Resource Report Resource Website 1+ mentions |
loadBAM2ge_db (RRID:SCR_015951) | software application, data visualization software, data processing software, software resource | Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer. | bam, map, mapping, genome, pipeline, maser, visualization, explorer | Public | SCR_015951 | loadBAM2ge_db (PE) | 2026-02-15 09:20:59 | 1 | ||||||||||
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Rickettsia Genome Database Resource Report Resource Website 1+ mentions |
Rickettsia Genome Database (RRID:SCR_007102) | database, data or information resource, image | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams. | evolutionary, africae, alignment, arthropod, bacteria, bellii, conorii, dendrogram, disease, genome, genomic, human, intracellular, massiliae, mechanism, pathogenicity, physiology, prowazekii, rickettsia, sequence, specie, journal article, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20993 | SCR_007102 | RicBase | 2026-02-15 09:19:22 | 1 | |||||||||
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Cerebellar Development Transcriptome Database Resource Report Resource Website 1+ mentions |
Cerebellar Development Transcriptome Database (RRID:SCR_013096) | CDT-DB | atlas, data or information resource, database | Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. | gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development |
is related to: Gene Ontology is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
Brain development, Brain disorder | INCF Japan Node ; Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:18603407 | To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. | nif-0000-00008 | SCR_013096 | 2026-02-15 09:20:40 | 1 | |||||
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Genomic HyperBrowser Resource Report Resource Website 10+ mentions |
Genomic HyperBrowser (RRID:SCR_010909) | Genomic HyperBrowser | service resource, analysis service resource, data analysis service, production service resource | A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets. | genomic, genomic track, gene regulation, disease association, epigenetic modification, genome |
is listed by: OMICtools has parent organization: University of Oslo; Oslo; Norway |
PMID:23632163 PMID:21182759 |
OMICS_00638 | SCR_010909 | The Genomic HyperBrowser | 2026-02-15 09:20:03 | 20 | |||||||
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UCSC Cancer Genomics Browser Resource Report Resource Website 500+ mentions |
UCSC Cancer Genomics Browser (RRID:SCR_011796) | Cancer Genomics Browser | data or information resource, database, service resource | A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets. | genome, genomics, clinical, next-generation sequencing, chromosome, gene, FASEB list |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
Cancer | NCI ; NHGRI ; American Association for Cancer Research ; UCSF Comprehensive Cancer Center ; California Institute for Quantitative Biosciences |
PMID:23109555 PMID:21059681 PMID:19333237 |
Acknowledgement requested | OMICS_00925 | SCR_011796 | 2026-02-15 09:20:24 | 530 | |||||
|
miRanda Resource Report Resource Website 100+ mentions |
miRanda (RRID:SCR_017496) | data or information resource, database, service resource | Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list | is listed by: SoftCite | NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.microrna.org/microrna/home.do | SCR_017496 | MicroRNA.org. microrna.org | 2026-02-15 09:22:07 | 210 | ||||||
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variation graph Resource Report Resource Website |
variation graph (RRID:SCR_024369) | vg | software toolkit, software resource | Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes. | read mapping, representing genetic variation in reference, encoding of sequences, genome | is listed by: Debian | PMID:30125266 | Free, Available for download, Freely available, | https://sources.debian.org/src/vg/ | SCR_024369 | variationgraph | 2026-02-15 09:22:41 | 0 | ||||||
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Four-dimensional Ascidian Body Atlas Resource Report Resource Website 1+ mentions |
Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) | FABA | atlas, data or information resource, d spatial image | Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate. | gene expression, genome, comparative genomics, human, microarray data, model organism, vertebrate, development, ascidian, embryonic development, embryo, video, developmental stage, 3d, slice, timelapse, egg, larva, time, confocal laser scanning microscopy | Japanese Ministry of Education Culture Sports Science and Technology MEXT ; JST-BIRD ; Japan Society for the Promotion of Science 18770207 |
PMID:17557317 | Free, Freely Available | nif-0000-02529 | http://ciona.lab.nig.ac.jp/ascidian/top.html | SCR_001691 | FABA: Four-dimensional Ascidian Body Atlas | 2026-02-15 09:18:09 | 5 | |||||
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GeneWiz browser Resource Report Resource Website 1+ mentions |
GeneWiz browser (RRID:SCR_001454) | service resource, analysis service resource, production service resource | An interactive web application for visualizing genomic data of sequenced prokaryotic chromosomes. It allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. | genome, chromosome, alignment, homologous gene, mapping, short sequencing reads, reference chromosome | has parent organization: Technical University of Denmark; Lyngby; Denmark | PMID:21304658 | Free, Freely Available | nif-0000-08429 | SCR_001454 | 2026-02-15 09:18:06 | 6 | ||||||||
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PhenoBank Resource Report Resource Website 1+ mentions |
PhenoBank (RRID:SCR_000930) | video resource, data or information resource, database | A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens. | phenotype, data, c elegans, genome, embryo, gonad, morphology, classification | has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_73232 | SCR_000930 | 2026-02-15 09:18:01 | 1 | |||||||||
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ERGO Resource Report Resource Website 50+ mentions |
ERGO (RRID:SCR_001243) | ERGO | service resource, analysis service resource, data analysis service, production service resource | A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement | genome analysis, genome, annotation, database, software, comparative genomics, function, gene, pathway, gene expression, microarray, FASEB list | is listed by: OMICtools | Restricted | OMICS_02097 | SCR_001243 | ERGO Genome Analysis and Discovery System, ERGO Genome Analysis & Discovery System | 2026-02-15 09:18:04 | 66 | |||||||
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Distant Regulatory Elements Resource Report Resource Website 10+ mentions |
Distant Regulatory Elements (RRID:SCR_003058) | DiRE | service resource, analysis service resource, data analysis service, production service resource | Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. | regulatory element, enhancer identification, genome, prediction, transcription factor binding site, gene, co-expression, co-function, function, transcription factor, comparative genomics, regulatory function, gene locus, chromosome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NLM ; Intramural Research Program |
PMID:18487623 | Free, Freely available | nif-0000-30448, biotools:dire | https://bio.tools/dire | SCR_003058 | Distant Regulatory Elements of co-regulated genes | 2026-02-15 09:18:26 | 25 | ||||
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Human Gene Connectome Server Resource Report Resource Website 1+ mentions |
Human Gene Connectome Server (RRID:SCR_002627) | HGCS | service resource, analysis service resource, data analysis service, production service resource | An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways. | gene, disease, phenotype, genome, connectome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Human Gene Connectome |
PMID:23509278 | Free | nlx_156049, biotools:hgcs | https://bio.tools/hgcs | SCR_002627 | 2026-02-15 09:18:21 | 5 | ||||||
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Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, source code, software resource | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software https://bio.tools/ancestrymap |
http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-02-15 09:18:45 | 12 | ||||
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Computational Biology at ORNL Resource Report Resource Website |
Computational Biology at ORNL (RRID:SCR_005710) | Computational Biology at ORNL | service resource, analysis service resource, data analysis service, production 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 | 2026-02-15 09:19:01 | 0 | ||||||||
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GOtcha Resource Report Resource Website 1+ mentions |
GOtcha (RRID:SCR_005790) | GOtcha | service resource, analysis service resource, data analysis service, production service resource | GOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online tool | function, protein, prediction, genome, annotation, gene, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Dundee; Scotland; United Kingdom |
Wellcome Trust 060269; European Union fifth framework QLRI-CT-2000-00127 |
PMID:15550167 | Free for academic use | nlx_149269 | http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html | SCR_005790 | 2026-02-15 09:19:03 | 1 | |||||
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Systems Transcriptional Activity Reconstruction Resource Report Resource Website 5000+ mentions |
Systems Transcriptional Activity Reconstruction (RRID:SCR_005622) | STAR | data or information resource, database, service resource | A next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets. | genome browser, genome, next generation sequence, visualization, FASEB list |
is used by: CIRCexplorer is listed by: OMICtools is related to: star-for-criu has parent organization: University of California at San Diego; California; USA |
Account required, Or Guest login | OMICS_00895 | SCR_005622 | Systems Transcriptional Activity Reconstruction Genome Browser, Systems Transcriptional Activity Reconstruction, STAR Genome Browser | 2026-02-15 09:19:00 | 6475 | |||||||
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Genomes Online Database Resource Report Resource Website 100+ mentions |
Genomes Online Database (RRID:SCR_002817) | GOLD | database, service resource, storage service resource, data repository, data or information resource | Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data. | genome, genetics, metagenome, biosample, phenotype, ecotype, disease, sequencing, FASEB list |
is listed by: re3data.org has parent organization: DOE Joint Genome Institute |
PMID:22135293 PMID:19914934 PMID:17981842 PMID:16381880 PMID:11125068 PMID:10498782 |
Free, Freely available, Available for download | r3d100010808, nif-0000-02918 | https://doi.org/10.17616/R39310 | SCR_002817 | Genomes On Line Database (GOLD), GOLD:Genomes Online Database | 2026-02-15 09:18:23 | 159 | |||||
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GeneSpeed- A Database of Unigene Domain Organization Resource Report Resource Website |
GeneSpeed- A Database of Unigene Domain Organization (RRID:SCR_002779) | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource, resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Database and customized tools to study the PFAM protein domain content of the transcriptome for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans tethered to both a genomics array repository database and a range of external information resources. GeneSpeed has merged information from several existing data sets including the Gene Ontology Consortium, InterPro, Pfam, Unigene, as well as micro-array datasets. GeneSpeed is a database of PFAM domain homology contained within Unigene. Because Unigene is a non-redundant dbEST database, this provides a wide encompassing overview of the domain content of the expressed transcriptome. We have structured the GeneSpeed Database to include a rich toolset allowing the investigator to study all domain homology, no matter how remote. As a result, homology cutoff score decisions are determined by the scientist, not by a computer algorithm. This quality is one of the novel defining features of the GeneSpeed database giving the user complete control of database content. In addition to a domain content toolset, GeneSpeed provides an assortment of links to external databases, a unique and manually curated Transcription Factor Classification list, as well as links to our newly evolving GeneSpeed BetaCell Database. GeneSpeed BetaCell is a micro-array depository combined with custom array analysis tools created with an emphasis around the meta analysis of developmental time series micro-array datasets and their significance in pancreatic beta cells. | molecular neuroanatomy resource, drosophila melanogaster, genome, caenorhabditis elegans, c. elegans, genomics, homo sapiens, mus musculus, protein domain, transcriptome |
is related to: Gene Ontology is related to: InterPro is related to: Pfam is related to: UniGene has parent organization: University of Colorado Denver; Colorado; USA |
NIDDK P30DK57516; NIDDK DK61248 |
PMID:17132830 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02887 | http://genespeed.uchsc.edu/, http://genespeed.ccf.org | SCR_002779 | GeneSpeed Database | 2026-02-15 09:18:23 | 0 |
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