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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PeakAnalyzer Resource Report Resource Website 1+ mentions |
PeakAnalyzer (RRID:SCR_001194) | PeakAnalyzer | software resource | A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution. | genome, chip, signal peak, binding site, modification site, enrichment loci, peak region, sequence, motif, chip-seq, chip-chip, c++, java, linux, mac os x, windows, bed, gtf, annotation, r, high-throughput sequencing, chromatin binding, modification loci, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:20691053 | Free, Available for download, Freely available | biotools:peakanalyzer, OMICS_02156 | https://bio.tools/peakanalyzer | SCR_001194 | 2026-08-01 12:01:34 | 3 | ||||||
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Breakway Resource Report Resource Website |
Breakway (RRID:SCR_001180) | Breakway | software resource | A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives. | genome, structural variation, breakpoint |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at Los Angeles; California; USA |
PMID:20126413 | Free, Available for download, Freely available | OMICS_02176 | SCR_001180 | Breakway: Identify Structural Variations in Genomic Data | 2026-08-01 12:01:41 | 0 | ||||||
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MuTect Resource Report Resource Website 50+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | Mutect | 2026-08-01 12:01:25 | 91 | ||||
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Reprever Resource Report Resource Website |
Reprever (RRID:SCR_000463) | Reprever | software resource | Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number. | genomics, genomic region, insertion breakpoint, insertion, breakpoint, duplicon, genome |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at San Diego; California; USA |
PMID:23658221 | Free, Available for download, Freely available | OMICS_01561 | SCR_000463 | Reprever: resolving low-copy duplicated sequences using template drive | 2026-08-01 12:01:14 | 0 | ||||||
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SciRoKo Resource Report Resource Website 1+ mentions |
SciRoKo (RRID:SCR_000941) | software resource | Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output. | genomics, comparative, genome, microsatellite, analysis, investigation | is listed by: OMICtools | PMID:17463017 | Free, Available for download, Freely available | OMICS_00113 | SCR_000941 | 2026-08-01 12:01:27 | 6 | ||||||||
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Functional Biosciences Resource Report Resource Website 1+ mentions |
Functional Biosciences (RRID:SCR_000943) | service resource | A service that provides low cost DNA sequencing. They utilize microfluidic technology. | dna, sequencing, sequence, gene, genome, microfluidic, technology | is listed by: ScienceExchange | SciEx_9422 | http://www.scienceexchange.com/facilities/functional-biosciences-inc | SCR_000943 | Functional Biosciences Inc. | 2026-08-01 12:01:33 | 2 | ||||||||
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Genome Canada Resource Report Resource Website 10+ mentions |
Genome Canada (RRID:SCR_000966) | Genome Canada | nonprofit organization | Genome Canada is a non-profit organization that is funded by the Government of Canada. The organization funds large-scale science and technology to fuel innovation regarding genomics in multiple sectors such as health, agriculture and agri-food, forestry, fisheries and aquaculture, environment, energy and mining. They create partnerships at the program and research project levels. | genome, genomics, funding, non profit, non-profit, innovation, health, agriculture, agri-food, agri food, forestry, fisheries, aquaculture, environment, energy, mining | is related to: Structural Genomics Consortium | Available to the research community | Crossref funder ID: 100008762, nlx_151964, Wikidata: Q3123000, ISNI: 0000 0001 0352 8618, grid.440163.4 | https://ror.org/029s29983 | SCR_000966 | 2026-08-01 12:01:34 | 11 | |||||||
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JBrowse Resource Report Resource Website 10+ mentions |
JBrowse (RRID:SCR_001004) | JBrowse | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. | genome |
is used by: Genome Resources for Yeast Chromosomes is listed by: OMICtools is listed by: Debian has parent organization: Broad Institute |
NHGRI 5R01HG004483-09 | PMID:22517427 PMID:21221095 |
GNU Lesser General Public License, Account required | OMICS_00918 | https://sources.debian.org/src/jbrowse/ | SCR_001004 | 2026-08-01 12:01:29 | 32 | |||||
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Patchwork Resource Report Resource Website 1+ mentions |
Patchwork (RRID:SCR_000072) | Patchwork | software resource | Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data. | genome, allele, copy number, bam, unix, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Uppsala University; Uppsala; Sweden |
Cancer, Tumor | PMID:23531354 | Free, Available for download, Freely available | biotools:patchwork, OMICS_02118 | https://bio.tools/patchwork | SCR_000072 | 2026-08-01 12:01:09 | 9 | |||||
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UnSplicer Resource Report Resource Website 1+ mentions |
UnSplicer (RRID:SCR_000226) | software resource | An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight. | RNA, sequencing, alignment, short reads, genome, genemark-es, gene prediction |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
PMID:24259430 | Free, Available for download, Freely available | OMICS_01806 | SCR_000226 | 2026-08-01 12:01:09 | 1 | ||||||||
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959 Nematode Genomes Resource Report Resource Website 1+ mentions |
959 Nematode Genomes (RRID:SCR_006068) | NematodeGenomes | narrative resource, data or information resource, wiki | A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs. | nematode, genome, genome sequencing, transcriptome sequencing, blast, genomics, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: nematodes.org has parent organization: University of Edinburgh; Scotland; United Kingdom |
NERC | PMID:22058131 | nlx_151473, biotools:959_nematode_genomes | https://bio.tools/959_nematode_genomes | SCR_006068 | NematodeGenomes | 2026-08-01 12:03:03 | 2 | |||||
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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 | 2026-08-01 12:03:08 | 0 | |||||
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TSSer Resource Report Resource Website |
TSSer (RRID:SCR_006419) | TSSer | software resource | A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide. | differential rna sequencing, transcription start site, rna-seq, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Basel; Basel; Switzerland |
PMID:24371151 | GNU General Public License | biotools:tsser, OMICS_02191 | https://bio.tools/tsser | SCR_006419 | TSSer: a computational pipeline to identify transcription start sites in bacterial genomes | 2026-08-01 12:03:11 | 0 | |||||
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Consensus Measures for Phenotype and Exposure Resource Report Resource Website 1+ mentions |
Consensus Measures for Phenotype and Exposure (RRID:SCR_006688) | PhenX | knowledge environment | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 05 01 2025. PhenX is a project to prioritize Phenotype and eXposure measures for Genome-wide Association Studies (GWAS). Leaders of the scientific community will assess and prioritize a broad range of domains relevant to genomics research and public health. The PhenX Steering Committee (SC), chaired by Dr. Jonathan Haines, provides leadership in the selection of domains and domain experts. Members of the SC include outstanding scientists from the research community and liaisons from the Institutes and Centers of the National Institutes of Health. Consensus measures for GWAS will have a direct impact on biomedical research and ultimately on public health. During the course of this project, up to 20 research domains will be examined, with up to 15 measures being recommended for use in future GWAS and other large-scale genomic research efforts. The goal is to maximize the benefits of future research by having comparable measures so that studies can be integrated. Each selected domain will be reviewed by a Working Group (WG) of scientists who are experts in the research area. A systematic review of the literature will guide the WGs selection of up to 15 high priority measures with standardized approaches for measurement. Selection criteria for the measures include factors such as validity, reproducibility, cost, feasibility, and burden to both investigators and participants. The scientific community will be asked to provide input on proposed measures. Consensus development is a key component of the project. | biomedical, domain, genome, health, phenotype, public, research |
has parent organization: RTI International is parent organization of: Phenotypes and eXposures Toolkit is parent organization of: PhenX Phenotypic Terms has organization facet: Phenotypes and eXposures Toolkit |
NHGRI U01 HG004597 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-32816 | SCR_006688 | PhenX - consensus measures for Phenotypes and eXposures, Consensus Measures for Phenotypes Exposures, PhenX (consensus measures for Phenotypes and eXposures), Consensus Measures for Phenotypes Exposure, Consensus Measures for Phenotypes and Exposures | 2026-08-01 12:03:17 | 1 | ||||||
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Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software resource, software application | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-08-01 12:10:44 | 274 | ||||||
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The Cancer Genome Atlas Resource Report Resource Website 5000+ mentions |
The Cancer Genome Atlas (RRID:SCR_003193) | TCGA | biomaterial supply resource, material resource | Project exploring the spectrum of genomic changes involved in more than 20 types of human cancer that provides a platform for researchers to search, download, and analyze data sets generated. As a pilot project it confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Its success committed resources to collect and characterize more than 20 additional tumor types. Components of the TCGA Research Network: * Biospecimen Core Resource (BCR); Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient. * Genome Characterization Centers (GCCs); Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers. * Genome Sequencing Centers (GSCs); High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer. * Proteome Characterization Centers (PCCs); The centers, a component of NCI's Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples. * Data Coordinating Center (DCC); The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal. * Cancer Genomics Hub (CGHub); Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments. * Genome Data Analysis Centers (GDACs) - Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data. TCGA is actively developing a network of collaborators who are able to provide samples that are collected retrospectively (tissues that had already been collected and stored) or prospectively (tissues that will be collected in the future). | genome, genome sequencing, breast, central nervous system, endocrine, gastrointestinal, gynecologic, head, neck, hematologic, skin, soft tissue, thoracic, urologic, clinical, genomic characterization, analysis, tumor genome, demographic, gene expression, copy number alteration, epigenetic, dna sequence, exome, snp, methylation, mrna, mirna, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: BioXpress is used by: cancerRxTissue is listed by: One Mind Biospecimen Bank Listing is related to: Cancer3D is related to: Cancer Research Data Commons is related to: CancerMIRNome is related to: Broad Institute Genomics Platform has parent organization: National Cancer Institute works with: FireBrowse |
Cancer, Tumor, Normal, Breast cancer, Central Nervous System cancer, Endocrine cancer, Gastrointestinal cancer, Gynecologic cancer, Head cancer, Neck cancer, Hematologic cancer, Skin cancer, Soft tissue cancer, Thoracic cancer, Urologic cancer | NCI 261200800001E-12-0-1 | nlx_156913 | SCR_003193 | Cancer Genome Atlas | 2026-08-01 12:10:43 | 6292 | ||||||
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DNAPlotter Resource Report Resource Website 100+ mentions |
DNAPlotter (RRID:SCR_005006) | DNAPlotter | software resource, software application | Software application used to generate images of circular and linear DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly. As this uses Artemis it can read in the common file formats EMBL, GenBank and GFF3. | java, circular, linear, plot, genome, macosx, unix, windows |
is listed by: OMICtools is related to: Artemis: Genome Browser and Annotation Tool has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:18990721 | GNU General Public License | OMICS_00906, nlx_96278 | SCR_005006 | DNAPlotter: circular and linear interactive genome visualization | 2026-08-01 12:10:50 | 108 | ||||||
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KI Biobank - TwinGene Resource Report Resource Website 10+ mentions |
KI Biobank - TwinGene (RRID:SCR_006006) | TwinGene | biomaterial supply resource, material resource | In collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo��protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed) | quantitative trait loci, environmental factor, cardiovascular disease, environment, genetic, gene, lipid syndrome, lipid, health, medication, questionnaire, c-reactive protein, total cholesterol, triglyceride, hdl, ldl, cholesterol, apolipo-protein a1, apolipo-protein b, glucose, hba1c, genome-wide linkage study, genome-wide association study, genome |
is listed by: One Mind Biospecimen Bank Listing is related to: GenomEUtwin is related to: Swedish Twin Registry has parent organization: Karolisnka Biobank |
Twin | NIH ; European Union ; VR ; SSF |
nlx_151387 | http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=31600&l=en | SCR_006006 | 2026-08-01 12:10:51 | 19 | ||||||
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Batch Entrez Resource Report Resource Website 10+ mentions |
Batch Entrez (RRID:SCR_016634) | software resource, software application | Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers. | load, number, genome, record, retrieval, nucleotide, sequence, protein, batch, mode |
has parent organization: NCBI works with: Entrez |
Public, Free, Freely available | SCR_016634 | 2026-08-01 12:11:07 | 47 | ||||||||||
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Human Genome Epidemiology Network Resource Report Resource Website 10+ mentions |
Human Genome Epidemiology Network (RRID:SCR_013117) | organization portal, data or information resource, portal | Human Genome Epidemiology Network, or HuGENet, is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. Its goals include: establishing an information exchange that promotes global collaboration in developing peer-reviewed information on the relationship between human genomic variation and health and on the quality of genetic tests for screening and prevention; providing training and technical assistance to researchers and practitioners interested in assessing the role of human genomic variation on population health and how such information can be used in practice; developing an updated and accessible knowledge base on the World Wide Web; and promoting the use of this knowledge base by health care providers, researchers, industry, government, and the public for making decisions involving the use of genetic information for disease prevention and health promotion. HuGENet collaborators come from multiple disciplines such as epidemiology, genetics, clinical medicine, policy, public health, education, and biomedical sciences. Currently, there are 4 HuGENet Coordinating Centers for the implementation of HuGENet activities: CDC''s Office of Public Health Genomics, Atlanta, Georgia; HuGENet UK Coordinating Center, Cambridge, UK; University of Ioannina, Greece; University of Ottawa , Ottawa, Canada. HuGENet includes: HuGE e-Journal Club: The HuGE e-Journal Club is an electronic discussion forum where new human genome epidemiologic (HuGE) findings, published in the scientific literature in the CDC''s Office of Public Health Genomics Weekly Update, will be abstracted, summarized, presented, and discussed via a newly created HuGENet listserv. HuGE Reviews: A HuGE Review identifies human genetic variations at one or more loci, and describes what is known about the frequency of these variants in different populations, identifies diseases that these variants are associated with and summarizes the magnitude of risks and associated risk factors, and evaluates associated genetic tests. Reviews point to gaps in existing epidemiologic and clinical knowledge, thus stimulating further research in these areas. HuGE Fact Sheets: HuGE Fact Sheets summarize information about a particular gene, its variants, and associated diseases. HuGE Case Studies: An on-line presentation designed to sharpen your epidemiological skills and enhance your knowledge on genomic variation and human diseases. Its purpose is to train health professionals in the practical application of human genome epidemiology (HuGE), which translates gene discoveries to disease prevention by integrating population-based data on gene-disease relationships and interventions. Students will acquire conceptual and practical tools for critically evaluating the growing scientific literature in specific disease areas. HUGENet Publications: Articles related to the HuGENet movement written by our HuGENet collaborators. HuGE Navigator: An integrated, searchable knowledge base of genetic associations and human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. HuGE Workshops: HuGENet has sponsored meetings and workshops with national and international partners since 2001. Available are detailed summaries, agendas or the ability to download speaker slides. HuGE Book: Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease. (The findings and conclusions in this book are those of the author(s) and do not necessarily represent the views of the funding agency.) HuGENet Collaborators: HuGENet is interested in establishing collaborations with individuals and organizations working on population based research involving genetic information. HuGE Funding: Funding opportunities for specific population-based genetic epidemiology research projects are available. Research initiatives whose aims include assessing the prevalence of human genetic variation, the association between genetic variants and human diseases, the measurement of gene-gene or gene-environment interaction, and the evaluation of genetic tests for screening and prevention are compiled to create a posted listing. Additional information and application details can be found by clicking on the respective links. | epidemiology, gene, genetic, genetic variants, genome, articles, collaboration, disease, disease prevention, genomics, health promotion, human, human diseases | has parent organization: Centers for Disease Control and Prevention | nif-0000-00574 | SCR_013117 | HuGENet | 2026-08-02 09:06:07 | 25 |
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