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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. | editing, database, management, plasmid maps, restriction, ligation, alignments, sequence, data, import, calculator, gel, image, display, PCR, cloning, genetic |
is listed by: Debian is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Free Software Foundation | Free, Available for download | OMICS_18307 | https://sources.debian.org/src/gentle/ | SCR_016127 | GENtle | 2026-09-12 12:58:35 | 6 | ||||||
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Tests for deviation from Hardy-Weinberg equilibrium Resource Report Resource Website 10+ mentions |
Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) | data analysis software, data processing software, software application, software resource | Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases. | deviation, Hardy-Weinberg, equilibrium, test, association, population, genetic, identify, susceptibility, gene, disease, single, nucleotide, polymorphisms, snp, allele | SCR_016496 | 2026-09-12 12:58:40 | 18 | ||||||||||||
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Cardiovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) | data or information resource, database, disease-related portal, portal, topical portal | Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data. | genetic, data, cardiovascular, disease, human | is listed by: NIDDK Information Network (dkNET) | cardiovascular disease, myocardial infarction, atrial fibrillation | Accelerating Medicines Partnership in Type 2 Diabetes ; National Institute of Cardiovascular Diseases and Stroke |
Free, Available for download, Google ID required, Tutorial available | SCR_016536 | 2026-09-12 12:58:41 | 31 | ||||||||
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MutaGene Resource Report Resource Website 10+ mentions |
MutaGene (RRID:SCR_016574) | data analysis software, data processing software, software application, software resource | Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity. | analyze, mutagenic, factor, turmor, decipher, cancer, genetic, heterogeneity | is listed by: OMICtools | National Library of Medicine ; NIH |
PMID:28472504 | Free, Available for download, Freely available | https://ncbiinsights.ncbi.nlm.nih.gov/tag/mutagene/ | SCR_016574 | 2026-09-12 12:58:41 | 10 | |||||||
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phyloscanner Resource Report Resource Website 1+ mentions |
phyloscanner (RRID:SCR_017400) | data analysis software, data processing software, software application, software resource | Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity. | Analysing, pathogen, genetic, diversity, relationship, host, genome | Bill & Melinda Gates Foundation ; ERC Advanced Grant ; Medical Research Council |
PMID:29186559 | Free, Available for download, Freely available | SCR_017400 | 2026-09-12 12:58:52 | 2 | |||||||||
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TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019. | temporal, signal, clocklikeness, molecular, phylogeny, visualization, analysis, temporally, sampled, sequenced, data, identify, genetic, incongruent | is related to: BEAST | ERC Grant ; EU Seventh Framework Programme |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | Path-O-Gen, tempest | 2026-09-12 12:58:51 | 166 | ||||||
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European Variation Archive (EVA) Resource Report Resource Website 100+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | data or information resource, data repository, database, service resource, storage service resource | Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser. | Collection, genetic, variation, data, chromosomal, location, dbSNP, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:eva | https://bio.tools/eva | SCR_017425 | EVA, European Variation Archive | 2026-09-12 12:58:52 | 107 | ||||||
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Cardiff Study of all Wales and North West of England Twins Resource Report Resource Website |
Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) | CaStANET | data or information resource | Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people. | Twins, family, genetic, environmental, origin, trait, collected, behavioral, psychopathological, data | PMID:17539361 | SCR_017480 | 2026-09-12 12:58:53 | 0 | ||||||||||
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GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | analysis service resource, atlas, data analysis service, data or information resource, database, production service resource, service resource | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | Gene ATLAS, Gene Atlas | 2026-09-12 12:58:54 | 158 | |||||||||
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GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | data analysis software, data processing software, software application, software resource | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-09-12 12:58:55 | 3 | |||||
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FaceBase Biorepository Resource Report Resource Website 1+ mentions |
FaceBase Biorepository (RRID:SCR_006001) | FaceBase Biorepository | biomaterial supply resource, material resource, tissue bank | THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. FaceBase Biorepository is now collecting biological samples from people with cleft lip/palate and their family members. Information for Prospective Cases: Clefts of the lip and/or palate can be caused by a wide range of genetic, environmental and other factors. The FaceBase Biorepository will serve as a common source of both biological samples and information that can be made available to investigators trying to determine the underlying cause of these common birth defects. Genetic studies, in particular, will benefit from both family history information and having samples from affected individuals as well as their family members. DNA is the information containing molecules found in all the cells of our body and can be easily obtained from material such as blood or saliva samples. As part of the FaceBase Biorepository, we are requesting families to submit biological samples from specific family members as well as information from other family members that might be affected with either the same condition or a similar condition. The medical and family history information that is collected includes other relevant information such as exposure to possible environmental causes during pregnancy. The biorepository is managed by Nichole Nidey, a research study coordinator, and Jeff Murray, a pediatric clinical geneticist and researcher. They are available to speak with family members regarding questions they may have, including providing information about the biorepository and making arrangements for the collection of samples for those who wish to participate. All participation is voluntary. Your name or other personally identifiable information (name, address, etc) will be removed before information is placed in the biorepository. Summary data to show how the database itself has been used overall as well as updates on whether specific findings might have been made using this database will be available on the FaceBase website at www.facebase.org. A newsletter containing this information will also be given to families and referring clinicians so that they may discuss the specifics with the families if there appears to be information that might be relevant in a particular case. Families will also need to sign a consent form that has been approved by the Institutional Review Board at the University of Iowa. Also, any submitted samples or data can also be removed from the database at any time should the family no longer wish to participate. Investigators interested in requesting DNA samples or for more information, please contact cleftresearch (at) uiowa.edu, Nichole Nidey, nichole-nidey (at) uiowa.edu or (319) 353-4365, or Jeff Murray, jeff-murray (at) uiowa.edu. | birth defect, genetic, environment, gene |
is listed by: One Mind Biospecimen Bank Listing has parent organization: FaceBase |
Cleft lip, Cleft palate, Family member, Campomelic Dysplasia, Chromosome Abnormality, Congenital Heart Disease, Facial clefting-Tessier Type 4, Gordon Syndrome, Hemifacial Microsomia, Idiopathic Short Stature, Marshall/Stickler, Microtia, Multiple Congenital Anomaly, Neurofibromatosis, Pierre Robin, Popliteal Pterygium Syndrome, Robinow, Downs syndrome, Townes-Brock Syndrome, Van der Woude Syndrome, Popliteal Pterygium Syndrome, Wildervanck Syndrome | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151379 | SCR_006001 | 2026-09-12 01:01:40 | 1 | |||||||
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YanHuang Project Resource Report Resource Website 50+ mentions |
YanHuang Project (RRID:SCR_006077) | data or information resource, database | This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided. | genome, genetic, adult, chromosome, clinical, control, genomic, human, normal, FASEB list | has parent organization: BGI; Shenzhen; China | nif-0000-03654 | SCR_006077 | YH1 | 2026-09-12 01:01:40 | 53 | |||||||||
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Atlas of Living Australia Resource Report Resource Website 100+ mentions |
Atlas of Living Australia (RRID:SCR_006467) | ALA | data or information resource, database | Online repository of information about Australian plants, animals, and fungi. Development started in 2006. The Commonwealth Scientific and Industrial Research Organisation is organisation significantly involved in development of ALA. | data sharing, biodiversity, image, photograph, dna, conservation, natural resource, literature, nomenclature, australia, morphology, life stage, stage, behavior, reproduction, habitat, genetic, region, species, portal, data set, data analysis service, metadata standard, web service, image collection, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: CSIRO has parent organization: GBIF - Global Biodiversity Information Facility |
Creative Commons Attribution License, v3 Australia License, Provider content may be covered by other Terms of Use, Http://www.ala.org.au/about-the-atlas/terms-of-use/ | nlx_152016, DOI:10.26197, DOI:10.25504/FAIRsharing.2f66da, r3d100010918, DOI:10.17616/R3VG9S | https://doi.org/10.26197, https://dx.doi.org/10.26197, http://doi.org/10.17616/R3VG9S, https://fairsharing.org/10.25504/FAIRsharing.2f66da, https://doi.org/10.17616/R3VG9S | SCR_006467 | 2026-09-12 01:01:42 | 174 | |||||||
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Genotype-IBD Sharing Test Resource Report Resource Website 100+ mentions |
Genotype-IBD Sharing Test (RRID:SCR_006257) | GIST | resource, software application, software resource | Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix. | identical by descent, genotype, gene, genetic, genomic, unix, ms-windows, linux, linkage disequilibrium, linkage, association |
is listed by: Genetic Analysis Software has parent organization: Vanderbilt University; Tennessee; USA |
Vanderbilt Diabetes Center ; NHGRI HG00376; NIDDK DK62370; NHGRI N01-HG-15465 |
PMID:14872409 | nlx_154133 | http://phg.mc.vanderbilt.edu/content/gist | SCR_006257 | 2026-09-12 01:01:42 | 120 | ||||||
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LDGROUP Resource Report Resource Website |
LDGROUP (RRID:SCR_006282) | software application, software resource | Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154422, SCR_009368, nlx_154590 | http://www.fumihiko.takeuchi.name/publications.html | SCR_006282 | R/LDGROUP | 2026-09-12 01:01:42 | 0 | ||||||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 500+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | analysis service resource, data analysis service, production service resource, service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-09-12 01:01:44 | 524 | |||||
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MIPS Ustilago maydis Database Resource Report Resource Website 1+ mentions |
MIPS Ustilago maydis Database (RRID:SCR_007563) | data or information resource, database | The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite. | drug, environment, filamentous, functional, fungal, fungal genome databases, fungus, gene, genetic, basidiomycete, cell, codon, culture, dikaryotic, diploid, genome, genomic, germinate, haploid, host, human, infection, maize, mating, meiotic, model, molecular, morphogenesis, network, orf, pathogen, pathologist, phytopathogen, phytopathogenesis, plant, protein, recombination, sequence, signal, spore, strain, structure, teliospore, teosinte, tissue, tumor, ustilago maydis, virulence, yeast | nif-0000-21276 | SCR_007563 | MUMDB | 2026-09-12 01:01:47 | 9 | ||||||||||
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POOLSCORE Resource Report Resource Website |
POOLSCORE (RRID:SCR_007514) | software application, software resource | Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | SCR_009373, nlx_154595, nlx_154087 | SCR_007514 | R/POOLSCORE | 2026-09-12 01:01:47 | 0 | |||||||||
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Ontology for Genetic Interval Resource Report Resource Website |
Ontology for Genetic Interval (RRID:SCR_003423) | OGI | controlled vocabulary, data or information resource, ontology | An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure. | owl, genomic, genetic, dna, rna, allele, marker, chromosome, rna molecule |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157517 | https://bioportal.bioontology.org/ontologies/OGI | SCR_003423 | 2026-09-12 01:00:09 | 0 | |||||||
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UC Davis Genome Center Labs and Facilities Resource Report Resource Website 1+ mentions |
UC Davis Genome Center Labs and Facilities (RRID:SCR_012480) | UCD Genome Center Labs & Facilities, UCD Genome Center Labs and Facilities | access service resource, core facility, data or information resource, organization portal, portal, service resource, training service resource | Genome Center uses technologies to understand how heritable genetic information of diverse organisms functions in health and disease. Provides research facilities, service cores, and staff for genomics research and training. Core facilities for Bioinformatics,DNA Technologies and Expression Analysis, Metabolomics, Proteomics,TILLING Core,Yeast One Hybrid Services Core. | Heritable, genetic, information, diverse, organism, function, health, disease, core, facility, service, genomic, training, |
is listed by: ScienceExchange is related to: University of California at Davis Genome Center Proteomics Core Facility has parent organization: University of California at Davis; California; USA |
SciEx_227, SCR_012659, SciEx_756 | https://genomecenter.ucdavis.edu/ | http://www.scienceexchange.com/facilities/uc-davis-genome-center-uc-davis | SCR_012480 | University of California Davis Genome Center Labs and Facilities, UC Davis Genome Center Labs & Facilities, University of California Davis Genome Center Labs & Facilities | 2026-09-12 01:00:15 | 3 |
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