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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SNPMSTAT Resource Report Resource Website |
SNPMSTAT (RRID:SCR_013339) | SNPMSTAT | software application, software resource | A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154647 | SCR_013339 | SNP Missing data STATistics | 2026-09-19 12:58:09 | 0 | ||||||||
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MECPM Resource Report Resource Website |
MECPM (RRID:SCR_013341) | MECPM | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154070 | SCR_013341 | Maximum Entropy Conditional Probability Moldeling | 2026-09-19 12:58:09 | 0 | ||||||||
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MAOS Resource Report Resource Website 10+ mentions |
MAOS (RRID:SCR_013351) | software application, software resource | Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++ | is listed by: Genetic Analysis Software | nlx_154452 | SCR_013351 | Meta-Analysis with Overlapping Subjects | 2026-09-19 12:58:09 | 25 | |||||||||
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Harvest-tools Resource Report Resource Website 1+ mentions |
Harvest-tools (RRID:SCR_016132) | software resource, software toolkit | Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. | archiving, postprocessing, reference, compressed, genomic, multialignment, create, interface, Gingr, file, phylogentic, tree, annotation, bioinformatic, format |
is listed by: Debian is listed by: OMICtools |
Department of Homeland Security Science and Technology Directorate | PMID:25410596 | Free, Available for download, Freely available | OMICS_08468 | https://github.com/marbl/harvest-tools, https://sources.debian.org/src/harvest-tools/ | SCR_016132 | 2026-09-19 12:58:14 | 4 | ||||||
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Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) Resource Report Resource Website 10+ mentions |
Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) | SALK IGC, IGC | access service resource, core facility, service resource | Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications. | core facility, gene, genomic, genomic data, analysis, consultation, applications | Helmsley Trust ; NCI CA014195; Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility |
Open | SCR_014842 | , Integrative Genomics, Salk, Core Facility, Institute, Razavi Newman, UCSD, Bioinformatics | 2026-09-19 12:59:15 | 38 | ||||||||
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Virginia Tech Biocomplexity Institute Genomics Sequencing Center Core Facility Resource Report Resource Website 1+ mentions |
Virginia Tech Biocomplexity Institute Genomics Sequencing Center Core Facility (RRID:SCR_017958) | GSC | access service resource, core facility, service resource | Core for development and application of Next-Generation Sequencing technologies. Provides experimental design consultation, and genomic, transcriptomic, and functional-genomics services. Specializes in development and application of Next-Generation Sequencing technologies and bioinformatics analyses. Instruments include Illumina NovaSeq 6000, Illumina NextSeq 500,Illumina MiSeq,Thermo Ion S5. Services include mRNA-Seq: Stranded and non-stranded, high levels of multiplexing up to 96 or more samples on NovaSeq;Standard amounts, Stranded-Seq: 500 ng total RNA, RIN 8;Low Input amounts, Stranded-Seq: 5 ng to 100 ng total RNA;Ultra Low Input amounts, Non-Stranded-Seq: 1-1000 cells or 10 pg - 10 ng;Total RNA-Seq - Stranded: 5-250 ng;Small RNA-Seq: 1 ug, multiplexing up to 48 samples/NextSeq run;Partially degraded samples - Stranded and Non-Stranded: LCM, FFPE samples, both stranded and non-stranded, 50 -100 ng;Microbial rRNA depletion and RNA-Seq with amounts as low as 1-5 ug of total RNA;Whole Genome Sequencing;Human / Animal / Plant;Microbial;As low as 1 ng De novo Sequencing;Exome/Targeted capture re-sequencing: Enables high sequencing depths;Agilent and Illumina platforms;Human, Mouse, Canine and other species;Targeted re-sequencing: High levels of multiplexing up to 200 samples / MiSeq run;PCR Amplicon sequencing;Illumina and Agilent platforms;ChIP-Seq;Transcription factor analysis;Histone modifications;DNA Methylation;MeDIP- and MBD-Seq;MethylC-Seq;Agilent SureSelect MethylC-Seq;Nucleosome Mapping;FAIRE-Seq and DNAse I-Seq;16S / 18S / ITS amplicon sequencing;Whole Genome Metagenomic sequencing;Metatranscriptomic analysis;DNA/chromatin fragmentation by Covaris DNA / RNA quality analysis: BioAnalyzer / TapeStation assay, Qubit (Picogreen) assays;qPCR services. | Genomic, sequencing, next, generation, design, consultation, transcriptomic, functional, service, analysis, DNA, RNA, PCR, qPCR, core, ABRF | is listed by: ABRF CoreMarketplace | Open | ABRF_991 | SCR_017958 | Genomics Sequencing Center | 2026-09-19 12:59:35 | 2 | |||||||
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Oregon State University Center for Quantitative Life Sciences Core Facility Resource Report Resource Website 1+ mentions |
Oregon State University Center for Quantitative Life Sciences Core Facility (RRID:SCR_018373) | CQLS | access service resource, core facility, service resource, training service resource | Formerly Center for Genome Research and Biocomputing Core Facility. Functions and facilities include services in genomics, functional genomics, genotyping and imaging.Biocomputing facilities with computing infrastructure, which includes managed cloud and shared resources, data analyses and training are customized to individual needs, including genome assembly and annotation, analysis of RNAseq, GBS, and metagenomics data, and GPU-enabled deep learning analyses. | Genome, genomic, functional genomic, genotyping, imaging, biocomputing, data analysis, training, core facility, ABRF, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Oregon State University; Oregon; USA |
Open | ABRF_856 | https://coremarketplace.org/?FacilityID=856 | SCR_018373 | CGRB, Center for Genome Research and Biocomputing | 2026-09-19 12:59:35 | 2 | ||||||
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University of Cape Town Centre for Proteomic and Genomic Research (CPGR) Core Facility Resource Report Resource Website 1+ mentions |
University of Cape Town Centre for Proteomic and Genomic Research (CPGR) Core Facility (RRID:SCR_017158) | CPGR Core | access service resource, core facility, service resource | Services to life science and biotech communities in South Africa. Based in Cape Town, combine information about genomic and proteomic technologies with bio computational pipelines to create fit for purpose offerings for customers in academia and industry. | bioinformatics, omics, core, facility, genomic, protemic | Restricted | SCR_017158 | Centre for Proteomic and Genomic Research, CPGR, core facility, University of Cape Town, Center for Proteomic and Genomic Research | 2026-09-19 12:59:27 | 3 | |||||||||
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University of Missouri Genomics Technology Core Facility Resource Report Resource Website 10+ mentions |
University of Missouri Genomics Technology Core Facility (RRID:SCR_017778) | GTC | access service resource, core facility, service resource | Core research facility providing services in high-throughput DNA sequencing that includes staff experience in the construction of libraries for targeted amplicons, miRNA analysis, transcriptome profiling (RNA-Seq), whole exome sequencing (WES), epigenomic and genomic DNA analysis. Services in single cell library preparation are available using the 10x Genomics Chromium X system. In addition, spatial transcriptomics services using Visium HD arrays are provided. The GTC maintain and operate Illumina sequencing platforms; NovaSeq X Plus and MiSeq i100 instruments. | Genomic, metagenomic, DNA, Illumina, NGS, next-gen sequencing, Sanger, 10x Genomics, single cell | Open | ABRF_363 | SCR_017778 | , University of Missouri Genomics Technology Core, Genomics Core Facility | 2026-09-19 12:59:30 | 19 | ||||||||
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Duke University Sequencing and Genomic Technologies Core Facility Resource Report Resource Website 1+ mentions |
Duke University Sequencing and Genomic Technologies Core Facility (RRID:SCR_017748) | access service resource, core facility, service resource | Basic research oriented core provides genomic services.Services include Next Generation Sequencing Solutions,DNA and RNA sequencing, Illumina, PacBio, NGS Library preparation including single-cell RNA-seq, Nucleic Acid Extraction Services, total RNA extraction from blood samples in PAXgene tubes, total RNA extractions from cell pellets and miRNA extraction from serum/plasma. | Next, generation, sequencing, genomic, DNA, RNA, total RNA, extraction, blood, cell, miRNA, serum, plasma, service, core | Open | ABRF_263 | SCR_017748 | Duke Cancer Institute Sequencing and Genomic Technologies Shared Resource | 2026-09-19 12:59:29 | 1 | |||||||||
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Duke University Molecular Genomics Core Facility Resource Report Resource Website 1+ mentions |
Duke University Molecular Genomics Core Facility (RRID:SCR_017860) | MGC | access service resource, core facility, service resource | Core offers variety of experimental platforms to facilitate genomics research. Accredited as Duke Shared Resource facility offers experience with genetic, genomic and epigenomic study design and technology, working closely with researchers to customize experiments to meet their needs. Applications include 10x Genomics NGS library generation for both single cell and gDNA experiments, DNA methylation microarrays, SNP genotyping and copy number microarrays, and Taqman targeted SNP genotyping. | Genomic, epigenomic, design, technology, customize, experiment, library, single, cell, gDNA, DNA, methylation, microarray, SNP, genotyping, service, core, ABRF | is listed by: ABRF CoreMarketplace | ABRF_682 | SCR_017860 | Molecular Genomics Core | 2026-09-19 12:59:32 | 2 | ||||||||
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University of California at San Francisco Embryonic Stem Cell Targeting Core Facility Resource Report Resource Website |
University of California at San Francisco Embryonic Stem Cell Targeting Core Facility (RRID:SCR_017902) | access service resource, core facility, service resource | Core provides ES cell services with high probability of germline transmission. Offers ES cell targeting, genomic DNA extraction from 96-well plates, expansion of targeted ES cells, chromosome counts, and preparation of ES cells for microinjection.Prior to initiation of project, consultation is available on entire procedures of generating knockout mice. Core works with Gladstone Transgenic Gene Targeting Core for your microinjections to deliver full-range gene targeting service;CRISPR gRNA cloning,Cell-based functional test to identify best-performing TALENs or sgRNAs for your gene-editing experiment via mismatch-based assays such as Surveyor or T7E1;In vitro RNA synthesis - can help to make RNAs for your zygote injection or RNA transfection. We have TALEN and Cas9 plasmids with either T7 or T3 promoter subcloned in for efficient in vitro synthesis.sgRNAs for CRISPR can be synthesized off T7-sgRNA PCR product. Quality of synthesized RNAs will be checked via bioanalyzer;Custom TALEN to make double-strand breaks in genome;ES cell targeting (feeder-independent).Investigators targeting construct will be electroporated by core personnel. We have two feeder-independent ES cell lines, E14 (129-derived) and JM8A3.N1 (C57BL/6-derived) you can choose from. After drug selection for about one week, up to 300 colonies will be picked. When they are about to be confluent, we will split them as duplicate, one master plate to freeze for future expansion of positive clones and one plate for genotyping to identify targeted ES cell clones. Your plates for genotyping will be ready for pick-up 2-3 weeks after electroporation date.Genomic DNA extraction from ES cells on 96-well plate;Expansion of targeted clones from core targeting (up to 5 clones),A maximum of 5 positive clones will be thawed from 96-well plates and expanded to 6-wells. We will freeze 5 vials (each about 1 million)/clone for future use and give you 1 vial-equivalent cells to validate your genotyping before injection. It takes about 10 days to expand and freeze down cells;Expansion of ES cells from outside resources (per clone) Investigators provide one vial of frozen ES cells with information about culture condition from original resource. We will revive, nurture, and refreeze ES cells (5 vials) when they are ready. In addition, we will give you 1~2 million cells for your genotyping verification;Preparation for microinjection;Chromosome counting;Custom services. | Cell, targeting, embryonic, stem, cell, germline, transmission, genomic, DNA, extraction, microinjection, knockout, mouse, generation, project, consultation, custom, service, core, ABRF | is listed by: ABRF CoreMarketplace | Restricted | ABRF_779 | SCR_017902 | UCSF ES Cell Targeting Core | 2026-09-19 12:59:33 | 0 | ||||||||
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GENERA Resource Report Resource Website 1+ mentions |
GENERA (RRID:SCR_023113) | data or information resource, narrative resource, training material, workflow | Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. | Genomic, Genome assembly, Phylogeny, Phylogenomic, comparative genomic, metabolic analyses, prokaryotes, eukaryotes | Free, Available for download, Freely available | SCR_023113 | GEN-ERA toolbox | 2026-09-19 12:55:30 | 9 | ||||||||||
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Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, software resource, source code | 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 | 2026-09-19 12:56:43 | 12 | ||||
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SGN Resource Report Resource Website 1000+ mentions |
SGN (RRID:SCR_004933) | SGN, SGN ref | data or information resource, database | A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions. | database, clade, genomic, sequence, phenotype, pathway, genetic, taxonomy, annotation, blast, plant genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Sol Genomics Network - Bulk download is related to: AmiGO has parent organization: Boyce Thompson Institute for Plant Research |
USDA ; ATC Inc. Advanced Technologies Cambridge ; NSF 0116076; NSF 9872617; NSF 975866; NSF 0421634 |
PMID:20935049 PMID:16010005 |
Public, The community can contribute to this resource | r3d100012078, nlx_89764, biotools:sol_genomics_network | https://bio.tools/sol_genomics_network, https://doi.org/10.17616/R3FS95 | http://www.sgn.cornell.edu/ | SCR_004933 | SGN ref, Sol Genomics Network | 2026-09-19 12:56:47 | 1261 | |||
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TranspoGene Resource Report Resource Website 1+ mentions |
TranspoGene (RRID:SCR_005634) | data or information resource, database | A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. | element, eukaryotic, evolutionary, exon, exonization, family, fruit fly, gene, genome, alternative, chicken, coding, disease, divergence, genomic, hosting, human, human genome databases, intron, location, map, maps, mouse, mrna, nematode, organism, pattern, promoter, protein, sea squirt, sequence, splicing, transcript, transcriptome, transposed, viewers, worm, zebrafish | has parent organization: Tel Aviv University; Ramat Aviv; Israel | nif-0000-03579 | SCR_005634 | TranspoGene | 2026-09-19 12:56:53 | 9 | |||||||||
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TRANSFAC Resource Report Resource Website 100+ mentions |
TRANSFAC (RRID:SCR_005620) | TRANSFAC | data or information resource, database | Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites. | Curated, eucaryotic, transcription, factor, genomic, binding, site, sequence, regulated, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: Gene Regulation Databases is related to: TRANSPATH is related to: Babelomics is related to: GeneTrail works with: rVista |
European Commission ; German Ministry of Education and Research |
PMID:12520026 | Free, Freely available | biotools:transfac, nif-0000-03576 | http://www.biobase-international.com/pages/index.php?id=transfac, http://gene-regulation.com/pub/databases.html, https://bio.tools/transfac | SCR_005620 | 2026-09-19 12:56:52 | 266 | |||||
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Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | Expression Profiler at the EBI | 2026-09-19 12:56:54 | 6 | ||||
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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 | 2026-09-19 12:56:56 | 9 | ||||
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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 | 2026-09-19 12:56:55 | 53 |
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