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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software resource, software application | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-02-14 02:07:00 | 370 | ||||||
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HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software resource, software application | A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, pedigree, haplotype, draw, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:15377505 | Free, Freely Available | nlx_154062, OMICS_00209, biotools:haplopainter | https://bio.tools/haplopainter | http://haplopainter.sourceforge.net/html/ManualIndex.htm | SCR_001710 | 2026-02-14 02:06:31 | 45 | |||||
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PEDHUNTER Resource Report Resource Website 1+ mentions |
PEDHUNTER (RRID:SCR_002031) | PedHunter | software resource, software application | Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot. | gene, genetic, genomic, genealogy, pedigree, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
PMID:20433770 PMID:9521925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pedhunter, OMICS_00211, nlx_154518 | https://bio.tools/pedhunter | SCR_002031 | 2026-02-14 02:06:41 | 2 | ||||||
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LAMP Resource Report Resource Website 1000+ mentions |
LAMP (RRID:SCR_001740) | LAMP | software resource, software application | Software for linkage and association modeling in pedigrees that uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern. | gene, genetic, genomic, c++, unix, linux, windows, macos, linkage, association, modeling, pedigree |
is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:16642434 | Free, Available for download, Freely available | nlx_154103 | SCR_001740 | Linkage and Association Modeling in Pedigrees | 2026-02-14 02:06:40 | 1157 | ||||||
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SYZYGY Resource Report Resource Website 1+ mentions |
SYZYGY (RRID:SCR_002157) | Syzygy | software resource, software application | A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software) | gene, genetic, genomic, variant calling, snp, indel, allele frequency, single-marker association, group-wise marker, quality control, variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Broad Institute |
PMID:21983784 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154668, OMICS_02166 | SCR_002157 | Syzygy - SNP and indel calling for pooled and individual targeted resequencing studies | 2026-02-14 02:06:54 | 5 | ||||||
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HWESTRATA Resource Report Resource Website |
HWESTRATA (RRID:SCR_001097) | HWESTRATA | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that calculates an exact stratified test for HWE for diallelic markers, such as single nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy Weinberg disequilbrium. In addition, exact tests for HWE are calculated for each stratum. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, solaris, ms-windows, (xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154405 | SCR_001097 | 2026-02-14 02:06:59 | 0 | ||||||||
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GAS2 Resource Report Resource Website |
GAS2 (RRID:SCR_001126) | GAS2 | software resource, software application | Software application for evaluating Statistical Significance in Two-Stage Genomewide Association Studies (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran77 | is listed by: Genetic Analysis Software | PMID:16408254 | nlx_154323 | SCR_001126 | statistical significance in Genomewide Association Studies in 2-stage | 2026-02-14 02:06:59 | 0 | |||||||
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EQTL EXPLORER Resource Report Resource Website 1+ mentions |
EQTL EXPLORER (RRID:SCR_001123) | EQTL EXPLORER | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | PMID:16357031 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154018 | SCR_001123 | 2026-02-14 02:06:39 | 2 | |||||||
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TDT-PC Resource Report Resource Website |
TDT-PC (RRID:SCR_001116) | TDT-PC | software resource, software application | Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, ms-dos, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
PMID:11443734 | nlx_154677, biotools:tdt_power_calculator | https://bio.tools/tdt_power_calculator | SCR_001116 | Transmission Disequilibrium Test Power Calculator, TDT Power Calculator | 2026-02-14 02:06:30 | 0 | ||||||
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BEAGLE Resource Report Resource Website 1000+ mentions |
BEAGLE (RRID:SCR_001789) | BEAGLE | software resource, software application | Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac). | gene, genetic, genomic, java, ms-windows, linux, unix, solaris, macos, identity by descent, genotype, haplotype |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:17924348 PMID:17326099 PMID:21310274 DOI:10.1086/521987 |
Free, Available for download, Freely available | nlx_154238, OMICS_00052, OMICS_00201 | https://sources.debian.org/src/beagle/ | https://www.stat.auckland.ac.nz/%7Ebrowning/beagle/beagle.html | SCR_001789 | BEAGLE Genetic Analysis Software Package | 2026-02-14 02:06:54 | 2197 | ||||
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CYRILLIC Resource Report Resource Website 50+ mentions |
CYRILLIC (RRID:SCR_001823) | Cyrillic | software resource, software application, commercial organization | Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages. | gene, genetic, genomic, visual c++, ms-windows, pedigree, linkage analysis, risk analysis, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software |
PMID:1973333 | Free, Available for download, Freely available | nlx_154279, OMICS_00208 | http://www.cyrillicsoftware.com | SCR_001823 | CyrillicSoftware | 2026-02-14 02:06:31 | 52 | |||||
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CLUSTAG Resource Report Resource Website 1+ mentions |
CLUSTAG (RRID:SCR_001816) | CLUSTAG | software resource, software application | Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment. | gene, genetic, genomic, java, hierarchical clustering, single nucleotide polymorphism, windows, unix |
is listed by: Genetic Analysis Software has parent organization: Hong Kong Baptist University; Hong Kong; China |
PMID:15585525 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154273 | http://hkumath.hku.hk/web/link/CLUSTAG/CLUSTAG.html | SCR_001816 | CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs | 2026-02-14 02:07:00 | 1 | |||||
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MILD Resource Report Resource Website 100+ mentions |
MILD (RRID:SCR_003335) | MILD | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software). | gene, genetic, genomic, unix, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154480 | SCR_003335 | MultIallelic Linkage Disequilibrium: a program for adjusted linkage disequilibrium (LD) calculations | 2026-02-14 02:06:34 | 106 | |||||||
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PAWE-3D Resource Report Resource Website 1+ mentions |
PAWE-3D (RRID:SCR_003326) | PAWE-3D | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | PMID:16123114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154481 | SCR_003326 | Power for Association With Error in 3D | 2026-02-14 02:07:03 | 2 | ||||||
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Toolbox at the European Bioinformatics Institute Resource Report Resource Website 50+ mentions |
Toolbox at the European Bioinformatics Institute (RRID:SCR_002872) | software resource, software toolkit | The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI. | expression, functional, gene, bioinformatics, database, genomic, homology, protein, proteomic, sequence, structural, toolbox | has parent organization: European Bioinformatics Institute | Free | nif-0000-25553 | SCR_002872 | EBI Bioinformatics Tools | 2026-02-14 02:06:56 | 85 | ||||||||
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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 | core facility, access service resource, 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 | 2026-02-14 02:08:40 | 2 | |||||||||
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University of Missouri-Columbia DNA Core Facility Resource Report Resource Website 10+ mentions |
University of Missouri-Columbia DNA Core Facility (RRID:SCR_017778) | DNACF | core facility, access service resource, service resource | Core research facility providing genomic services that include next generation sequencing , single cell sequencing, metagenomic, targeted amplicon sequencing, and Sanger sequencing. | Genomic, DNA, Illumina, sequencing, Sanger, fragment, analysis, 10x Genomics, Core Marketplace | is related to: USEDit | Open | ABRF_363 | SCR_017778 | DNA Core Facility | 2026-02-14 02:08:04 | 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) | core facility, access service resource, 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 | 2026-02-14 02:08:41 | 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 | core facility, access service resource, 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 | 2026-02-14 02:08:34 | 1 | ||||||||
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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) | core facility, access service resource, 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 | 2026-02-14 02:08:06 | 0 |
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