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http://discover.nci.nih.gov/gominer/

GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches.

Proper citation: GoMiner (RRID:SCR_002360) Copy   

•   Source: SciCrunch Registry

http://www.fged.org/

Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.

Proper citation: FGED (RRID:SCR_001897) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html

Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software)

Proper citation: LAPSTRUCT (RRID:SCR_007550) Copy   

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http://www.pedigree-draw.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software)

Proper citation: Pedigree-Draw (RRID:SCR_008302) Copy   

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http://bnmc.caltech.edu/

The Beckman Institute BNMC brings together researchers from many disciplines at Caltech to address problems in the mechanistic modeling of coupled genomic, intercellular and intracellular processes. It represents an attempt to encourage closer interaction and collaboration between groups in Biology, Control and Dynamical Systems, and the Center for Advanced Computing Research. The focus of BNMC is biochemical phenomena occurring within and between cells, in particular the mechanistic modeling of molecular networks of all kinds (e.g., transcriptional, regulatory, metabolic, signal transduction, mechanical, etc.) with and without spatial variation and intercellular communication. BNMC is formed as a coordinated effort aimed at (1) applying existing capabilities to collaboratively solve biological modeling problems that arise in answering scientific questions in Caltech laboratories, (2) exploring a diversity of novel approaches in order to achieve fundamental advances necessary to address the classes of modeling problems biologists want to solve, and (3) organizing projects to better share human experience as well as common infrastructure to avoid duplication and maximize solution interoperability.

Proper citation: Caltech, The Beckman Institute: The Biological Network Modeling Center (RRID:SCR_008060) Copy   

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https://cran.r-project.org/web/packages/ibdreg/index.html

Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software)

Proper citation: IBDREG (RRID:SCR_013127) Copy   

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https://nels.bioinfo.no

Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project.

Proper citation: NeLS (RRID:SCR_016301) Copy   

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http://wpicr.wpic.pitt.edu/WPICCompGen/blocks.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software)

Proper citation: ENTROPY BLOCKER (RRID:SCR_000123) Copy   

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http://www.acgtinc.com

Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels.

Proper citation: ACGT Inc. (RRID:SCR_001026) Copy   

•   Source: SciCrunch Registry

http://www.homozygositymapper.org/

A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry

http://weatherby.genetics.utah.edu/cgi-bin/Phevor/PhevorWeb.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles.

Proper citation: Phevor (RRID:SCR_002273) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/

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.

Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy   

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https://mugenomicscore.missouri.edu/

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.

Proper citation: University of Missouri Genomics Technology Core Facility (RRID:SCR_017778) Copy   

•   Source: SciCrunch Registry

https://genome.duke.edu/cores-and-services/sequencing-and-genomic-technologies

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.

Proper citation: Duke University Sequencing and Genomic Technologies Core Facility (RRID:SCR_017748) Copy   

•   Source: SciCrunch Registry

http://www.cpgr.org.za

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.

Proper citation: University of Cape Town Centre for Proteomic and Genomic Research (CPGR) Core Facility (RRID:SCR_017158) Copy   

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http://dmpi.duke.edu/molecular-genomics-shared-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.

Proper citation: Duke University Molecular Genomics Core Facility (RRID:SCR_017860) Copy   

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https://escore.ucsf.edu/

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.

Proper citation: University of California at San Francisco Embryonic Stem Cell Targeting Core Facility (RRID:SCR_017902) Copy   

•   Source: SciCrunch Registry

https://www.bi.vt.edu/services/genomics-sequencing-center

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.

Proper citation: Virginia Tech Biocomplexity Institute Genomics Sequencing Center Core Facility (RRID:SCR_017958) Copy   

•   Source: SciCrunch Registry

http://cqls.oregonstate.edu/

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.

Proper citation: Oregon State University Center for Quantitative Life Sciences Core Facility (RRID:SCR_018373) Copy   

•   Source: SciCrunch Registry

http://www.genyo.es/en

Center for excellence research in genomic medicine, focusing on the comprehensive study and understanding of the genetic basis of human diseases in general, placing special emphasis on cancer and its genetic disorders related to inheritance. GENYO was created as a multidisciplinary research space, where different professionals from the healthcare, university and business areas interact, making it possible to generate new systems to diagnose, prevent and treat diseases based on the joint and coordinated application of first-rate knowledge in the different areas of genetics. The center is the benchmark center of the Andalusian Program for Research in Clinical Genetics and Genomic Medicine, a program which, together with those of Cell Therapy and Regenerative Medicine, and Nanomedicine have the main objective of supporting and fostering translational research in Advanced Therapies. The activities performed within these three research programs are developed in coordination with the Andalusian Initiative for Advanced Therapies (IATA), an initiative of the Andalusian Government promoted by the Regional Ministries of Health and Innovation, Science and Enterprise.

Proper citation: Centre for Genomics and Oncological Research (RRID:SCR_003920) Copy   

•   Source: SciCrunch Registry