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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
tbrowse
 
Resource Report
Resource Website
tbrowse (RRID:SCR_001918) tbrowse software resource Software providing a HTML5/javascript based browser for visualizing RNA-seq results in the familiar track layout of common genome browser. But given the quantitative nature of RNA-seq data, in addition to visualizing sequence coverage, the browser quantitates transcript abundance across regions of interest. The HTML5 functionality is made of use to render all the tracks using the canvas drawing element. This greatly reduces the load on servers and allows for rich interactive graphics without the need for third-party plugins. Furthermore, this framework completely segregates data from visualization, making development much easier. The browser is designed to run on all modern browsers: Firefox, Safari, Chrome, Opera and Internet Explorer (though not recommended). genome, browser, transcriptome, html5, canvas, extjs, visualization, rna-seq is listed by: OMICtools
has parent organization: Google Code
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01935 SCR_001918 tbrowse - HTML5 Transcriptome Browser 2026-02-14 02:00:15 0
EBCall
 
Resource Report
Resource Website
10+ mentions
EBCall (RRID:SCR_006791) EBCall software resource A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. mutation, cancer, genome, sequencing, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Tokyo; Tokyo; Japan
PMID:23471004 Copyright conditions, Acknowledgement required biotools:ebcall, OMICS_00084 https://bio.tools/ebcall SCR_006791 EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling 2026-02-14 02:01:23 19
Genome Research Foundation
 
Resource Report
Resource Website
1+ mentions
Genome Research Foundation (RRID:SCR_006056) GRF, GF institution The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project bioinformatics, genomics, genome, genome sequencing, personalized medicine, personal genomics, angiogenesis, drug, rna expression, protein structure has parent organization: Korean Ministry of Education Science and Technology
is parent organization of: MetaBase
Content is available under BioLicense: the freest license. grid.410888.d, nlx_151458, Wikidata: Q5533483 https://ror.org/03khjyh83 SCR_006056 Genome Foundation 2026-02-14 02:01:02 1
estMOI
 
Resource Report
Resource Website
10+ mentions
estMOI (RRID:SCR_006192) estMOI software resource A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt). multiplicity of infection, parasite, genome, high throughput sequencing, single nucleotide polymorphism, chromosome is listed by: OMICtools PMID:24443379 Free, Public OMICS_02240 SCR_006192 estMOI - Estimating multiplicity of infection using parasite deep sequencing data 2026-02-14 02:01:14 10
HapCompass
 
Resource Report
Resource Website
1+ mentions
HapCompass (RRID:SCR_000942) algorithm Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings. algorithm, haplotype, sequence, genome, dna, rna, snp is listed by: OMICtools
has parent organization: Brown University; Rhode Island; USA
NSF 1048831;
NSF 1321000
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00197 SCR_000942 2026-02-14 01:59:52 1
Genome Trax
 
Resource Report
Resource Website
1+ mentions
Genome Trax (RRID:SCR_001234) Genome Trax service resource Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia. next-generation sequencing, genome, exome, sequence, variation, mutation, pathogenic, database, bio.tools, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: BIOBASE Corporation
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02109, biotools:genome_trax https://bio.tools/genome_trax SCR_001234 Genome Trax for Next Generation Sequencing 2026-02-14 01:59:58 2
TALLYMER
 
Resource Report
Resource Website
1+ mentions
TALLYMER (RRID:SCR_001244) Tallymer software resource A collection of flexible and memory-efficient software programs for k-mer counting and indexing of large sequence sets. It is based on enhanced suffix arrays which gives a much larger flexibility concerning the choice of the k-mer size. It can process large data sizes of several billion bases. k-mer, counting, sequence, genome annotation, genome, annotation, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Hamburg; Hamburg; Germany
PMID:18976482 Free, Freely available biotools:tallymer, OMICS_02096 https://bio.tools/tallymer SCR_001244 2026-02-14 02:00:03 7
ADMIXTURE
 
Resource Report
Resource Website
1000+ mentions
ADMIXTURE (RRID:SCR_001263) ADMIXTURE software resource A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. ancestry, macos x, linux, admixture, allele, genome, single nucleotide polymorphism, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of California at Los Angeles; California; USA
PMID:19648217 THIS RESOURCE IS NO LONGER IN SERVICE biotools:admixture, OMICS_02077 http://www.genetics.ucla.edu/software/admixture/ SCR_001263 ADMIXTURE: fast ancestry estimation 2026-02-14 01:59:59 2679
frappe
 
Resource Report
Resource Website
50+ mentions
frappe (RRID:SCR_001264) frappe software resource Software using a f frequentist approach for estimating individual ancestry proportion. ancestry, admixture, genome, allele is listed by: OMICtools
has parent organization: Stanford University School of Medicine; California; USA
PMID:15712363 Free, Available for download, Freely available OMICS_02076 SCR_001264 2026-02-14 02:00:04 55
Flash Gviewer
 
Resource Report
Resource Website
1+ mentions
Flash Gviewer (RRID:SCR_012870) Flash GViewer software resource Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Medical College of Wisconsin; Wisconsin; USA
Free for academic use nlx_149333 http://gmod.org/flashgviewer SCR_012870 2026-02-14 02:02:24 2
IGB
 
Resource Report
Resource Website
100+ mentions
IGB (RRID:SCR_011792) IGB software resource An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more. genome, rna-seq, chip-seq, tiling array, browser is listed by: OMICtools
has parent organization: University of North Carolina at Charlotte; North Carolina; USA
PMID:19654113 Free, Acknowledgement requested OMICS_00916 SCR_011792 Integrated Genome Browser 2026-02-14 02:02:26 336
GenomeJack
 
Resource Report
Resource Website
10+ mentions
GenomeJack (RRID:SCR_012026) GenomeJack software resource A genome browser specialized in next-generation sequencing data. next-generation sequencing, genome, browser, analysis is listed by: OMICtools Free, Public OMICS_02143 SCR_012026 2026-02-14 02:02:17 32
3D Genome
 
Resource Report
Resource Website
10+ mentions
3D Genome (RRID:SCR_017525) service resource Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. 3D, genome, organization, gene, regulation, data, visualization, chromatin, interaction, omic, ChIPseq, RNAseq, regulatory, structure is related to: Encode
has parent organization: Pennsylvania State University
THIS RESOURCE IS NO LONGER IN SERVICE SCR_017525 2026-02-14 02:03:21 20
GeneChip™ Scanner 3000 7G
 
Resource Report
Resource Website
1+ mentions
GeneChip™ Scanner 3000 7G (RRID:SCR_016522) instrument resource Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip Commercially available https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf SCR_016522 2026-02-14 02:03:05 1
SVDetect
 
Resource Report
Resource Website
10+ mentions
SVDetect (RRID:SCR_010812) SVDetect software resource Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads. structural variation, sequencing, chromosomal rearrangement, high-throughput sequencing, solid, illumina, genome, insertion, deletion, inversion, duplication, translocation, command-line, perl, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
has parent organization: Curie Institute; Paris; France
PMID:20639544 GNU General Public License, v3 OMICS_00324, biotools:svdetect https://bio.tools/svdetect SCR_010812 SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data 2026-02-14 02:01:50 23
Recon x
 
Resource Report
Resource Website
10+ mentions
Recon x (RRID:SCR_006345) Recon x data or information resource, database A comprehensive biochemical knowledge-base on human metabolism, this community-driven, consensus metabolic reconstruction integrates metabolic information from five different resources: * Recon 1, a global human metabolic reconstruction (Duarte et al, PNAS, 104(6), 1777-1782, 2007) * EHMN, Edinburgh Human Metabolic Network (Hao et al., BMC Bioinformatics 11, 393, 2010) * HepatoNet1, a liver metabolic reconstruction (Gille et al., Molecular Systems Biology 6, 411, 2010), * Ac/FAO module, an acylcarnitine/fatty acid oxidation module (Sahoo et al., Molecular bioSystems 8, 2545-2558, 2012), * a human small intestinal enterocytes reconstruction (Sahoo and Thiele, submitted). Additionally, more than 370 transport and exchange reactions were added, based on a literature review. Recon 2 is fully semantically annotated (Le Nov��re, N. et al. Nat Biotechnol 23, 1509-1515, 2005) with references to persistent and publicly available chemical and gene databases, unambiguously identifying its components and increasing its applicability for third-party users. Here you can explore the content of the reconstruction by searching/browsing metabolites and reactions. Recon 2 predictive model is available in the Systems Biology Markup Language format. metabolism, annotation, metabolite, reaction, genome, reconstruction has parent organization: University of Iceland; Reykjavik; Iceland Knut and Alice Wallenberg Foundation ;
Marie Curie International Reintegration Grant 249261;
European Research Council 232816;
Rannis research 100406022;
Manchester Centre for Integrative Systems Biology BB/C008219/1;
Bioprocessing Research Industry Club ;
European Union FP7 201142;
BBSRC BB/F005938;
BBSRC BB/F00561X;
DFG 0315756;
DFG 0315741;
NIGMS GM088244;
NSF 0643548;
Cystic Fibrosis Research Foundation 1060
PMID:23455439 Free, Acknowledgement requested nlx_152079 SCR_006345 Recon x Reconstruction of The Human Genome, Recon x - Reconstruction of The Human Genome, Recon x: Reconstruction of The Human Genome, Recon 2 2026-02-14 02:06:34 11
Mouse Genome Informatics (MGI)
 
Resource Report
Resource Website
1000+ mentions
Mouse Genome Informatics (MGI) (RRID:SCR_006460) MGI data or information resource, database International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI. RIN, Resource Information Network, molecular neuroanatomy resource, human health, human disease, animal model, gene expression, phenotype, genotype, gene, pathway, orthology, tumor, strain, single nucleotide polymorphism, recombinase, function, blast, image, pathology, model, data analysis service, genome, genetics, gold standard, RRID Community Authority uses: InterMOD
is used by: NIF Data Federation
is used by: Resource Identification Portal
is used by: PhenoGO
is used by: Integrated Animals
is used by: Cytokine Registry
is used by: NIH Heal Project
is recommended by: Resource Identification Portal
is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: 3DVC
is listed by: re3data.org
is listed by: OMICtools
is listed by: NIH Data Sharing Repositories
is listed by: InterMOD
is listed by: Resource Information Network
is affiliated with: InterMOD
is related to: MONARCH Initiative
is related to: MouseCyc
is related to: AmiGO
is related to: Gene Expression Database
is related to: Bgee: dataBase for Gene Expression Evolution
is related to: HomoloGene
is related to: Rat Gene Symbol Tracker
is related to: Enhancer Trap Line Browser
is related to: Integrated Brain Gene Expression
is related to: MalaCards
is related to: Gene Ontology
is related to: BioMart Project
is related to: NIH Data Sharing Repositories
is related to: RIKEN integrated database of mammals
is related to: JAX Neuroscience Mutagenesis Facility
is related to: PhenoGO
is related to: International Mouse Strain Resource
is related to: Mouse Genome Database
is related to: Mouse Tumor Biology Database
has parent organization: Jackson Laboratory
is parent organization of: Anatomy of the Laboratory Mouse
is parent organization of: Mouse Genome Informatics Transgenes
is parent organization of: Federation of International Mouse Resources
is parent organization of: MGI GO Browser
is parent organization of: Recombinase (cre) Activity
is parent organization of: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project
is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource
is parent organization of: MGI strains
is parent organization of: MPO
is parent organization of: Phenotypes and Mutant Alleles
is parent organization of: Human Mouse Disease Connection
is parent organization of: Functional Annotation
is parent organization of: Strains, SNPs and Polymorphisms
is parent organization of: Vertebrate Homology
is parent organization of: Batch Data and Analysis Tool
is parent organization of: Nomenclature
NHGRI HG000330;
NHGRI HG002273;
NICHD HD033745;
NCI CA089713
PMID:19274630
PMID:18428715
Free, Freely available nif-0000-00096, OMICS_01656, r3d100010266 http://www.informatics.jax.org/batch
http://www.informatics.jax.org/submit.shtml
http://www.informatics.jax.org/expression.shtml
https://doi.org/10.17616/R35P54
SCR_006460 , MGI, Mouse Genome Informatics 2026-02-14 02:05:55 1119
SNPedia
 
Resource Report
Resource Website
50+ mentions
SNPedia (RRID:SCR_006125) SNPedia data or information resource, database Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php dna, genetics, gene, genome, genoset, genotype, medicine, medical condition, genetic variation, dna, genetic variation, genomics, single nucleotide polymorphism, medical association, phenotypic association, genealogical association, variation, genome annotation, phenotype, web service, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
PMID:22140107 Creative Commons Attribution-NonCommercial-ShareAlike License, v3 biotools:snpedia, grid.465250.0, nlx_151604 https://ror.org/0253rdk33
https://bio.tools/snpedia
SCR_006125 2026-02-14 02:05:59 62
ProPortal
 
Resource Report
Resource Website
1+ mentions
ProPortal (RRID:SCR_006112) ProPortal data or information resource, database ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included. genomic, metagenomic, transcriptomic, field data, marine cyanobacterium, genome, ecosystem, ecotypic variation, microbial taxon, phage, genome, gene, orthologous gene cluster, cyanobacteria, cyanophage genome, population dynamics, microarray, metagenome, protein, cyanophage, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
NSF OCE-0425602;
NSF EF0424599;
DOE DE-FG02-02ER63445;
DOE DE-FG02-08ER64516;
DOE DE-FG02-07ER64506;
Gordon and Betty Moore Foundation award letter 495.01
PMID:22102570 Public nlx_151586, biotools:proportal https://bio.tools/proportal SCR_006112 Prochlorococcus Portal 2026-02-14 02:06:25 9
Clinical Genomic Database
 
Resource Report
Resource Website
1+ mentions
Clinical Genomic Database (RRID:SCR_006427) CGD data or information resource, database Manually curated database of all conditions with known genetic causes, focusing on medically significant genetic data with available interventions. Includes gene symbol, conditions, allelic conditions, inheritance, age in which interventions are indicated, clinical categorization, and general description of interventions/rationale. Contents are intended to describe types of interventions that might be considered. Includes only single gene alterations and does not include genetic associations or susceptibility factors related to more complex diseases. genomic sequencing, genome, clinical, pediatric, adult human, young human, genomic medicine, whole-genome sequencing, gene, organ system, intervention, gene symbol, condition, allelic condition, clinical categorization, manifestation, inheritance, age group, genetic variant, pathogenic mutation is used by: NIF Data Federation
has parent organization: National Human Genome Research Institute
NHGRI PMID:23696674 Free, Freely available nlx_152872, r3d100012332 https://doi.org/10.17616/R31D3C SCR_006427 Clinical Genomics Database 2026-02-14 02:05:55 9

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