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https://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May24,2023. Software program that implements the Mantel statistics as proposed by Beckmann et al. (2005) to test for association between genetic markers and phenotypes in case-control studies using haplotype information. The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take into account linkage disequilibrium information between multiple markers, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for space time clustering, which we developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. Alternative measures for the phenotypic similarity were implemented. (entry from Genetic Analysis Software)

Proper citation: TOMCAT (RRID:SCR_013120) Copy   

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http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software)

Proper citation: SASQUANT (RRID:SCR_013122) Copy   

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http://dlin.web.unc.edu/software/SCORE-Seq/

A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software)

Proper citation: SCORE-SEQ (RRID:SCR_013121) Copy   

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http://www.aps.uoguelph.ca/~msargol/qmsim/

Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software)

Proper citation: QMSIM (RRID:SCR_013123) Copy   

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http://www.stat.washington.edu/thompson/Genepi/InSegT.shtml

Software application that constructs feasible haplotype configurations and the corresponding segregation types on pedigrees. the haplotype configuration minimizes recombinations on the pedigree. (entry from Genetic Analysis Software)

Proper citation: INSEGT (RRID:SCR_013126) Copy   

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http://genome.sph.umich.edu/wiki/GlfSingle

Software application that is a GLF-based variant caller for next-generation sequencing data. It takes one/three/multiple GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output. (entry from Genetic Analysis Software)

Proper citation: GLFSINGLE/GLFTRIO/GLFMULTIPLES (RRID:SCR_013128) Copy   

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https://sourceforge.net/projects/ggsd/

Web-based, relational database driven data management software package for the management of large scale genetic studies. (entry from Genetic Analysis Software)

Proper citation: GGSD (RRID:SCR_013129) Copy   

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http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/chromscan/

A statistical based program for association mapping of disease genes. It utilises the Malecot model and the linkage disequilibrium (LD) map for the candidate region to analyse the genotypes derive from large sample of matched cases and controls. (entry from Genetic Analysis Software)

Proper citation: CHROMSCAN (RRID:SCR_013131) Copy   

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http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application to compute composite measures of linkage disequilibrium, their variances and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is unkown. An extension of Weir and Cockerham (1989) to apply to multi-allelic loci. (entry from Genetic Analysis Software)

Proper citation: COMPOSITELD (RRID:SCR_013132) Copy   

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http://faculty.washington.edu/eathomp/Anonftp/PANGAEA/BOREL/

Software application for inference of genealogical relationships from genetic data, including sibship inference.

Proper citation: BOREL (RRID:SCR_013135) Copy   

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http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software)

Proper citation: GASSOC (RRID:SCR_013136) Copy   

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http://dlin.web.unc.edu/software/SNPMStat/

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)

Proper citation: SNPMSTAT (RRID:SCR_013339) Copy   

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http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm

Software application (entry from Genetic Analysis Software)

Proper citation: MECPM (RRID:SCR_013341) Copy   

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http://www.bios.unc.edu/~lin/software/MAOS/

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)

Proper citation: MAOS (RRID:SCR_013351) Copy   

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https://neuinfo.org/mynif/search.php?list=cover&q=*

Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below.

Proper citation: NIF Data Federation (RRID:SCR_004834) Copy   

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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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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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http://www.iastate.edu/

Iowa State University (ISU) is an undergraduate, graduate and research institute. ISU has 100 majors and upwards of 800 student organizations.

Proper citation: Iowa State University; Iowa; USA (RRID:SCR_000972) Copy   

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http://www.feinsteininstitute.org/Feinstein/Feinstein+HomePage

The Feinstein Institute for Medical Research is the research branch of the North Shore-Long Island Jewish Health System. Biomedical research has been a vital aspect of its two academic medical centers North Shore University Hospital and Long Island Jewish Medical Center since their establishment in the early 1950''s. Through its connection to the hospital system, the Institute bridges the gap between biomedical research and patient care, accessing hundreds of thousands of patients in the health system''s 15 hospitals, four long-term care facilities, three trauma centers, six home health agencies and dozens of outpatient facilities. Institute scientists collaborate with clinicians throughout the system to shed light on basic biological processes underlying disease. This knowledge is used to develop new therapies and diagnostics. Currently, more than 800 scientists and investigators are conducting research in oncology, immunology and inflammation, genetics, psychiatry, neurology, pediatrics, surgery, urology, obstetrics/gynecology and many other specialties. In 2008, the Feinstein received funding from the National Institutes of Health in excess of $28 million, and an additional $10 million from other federal sources. Total annual research funding from all sources exceeded $44 million in 2008. We stand at the threshold of an extraordinary time in medicine. Over the last 100 years, biomedical science has progressed very rapidly. Advances coming from the integration of genomics, proteomics and bioinformatics into the biomedical toolkit hold the promise that this transformation will continue well into the 21st century. The Feinstein Institute for Medical Research is a growing force in research innovation, education and progress.

Proper citation: Feinstein Institute for Medical Research (RRID:SCR_004470) Copy   

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