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https://genenames.org

Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.

Proper citation: HGNC (RRID:SCR_002827) Copy   

•   Source: SciCrunch Registry

http://jaspar.genereg.net

Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.

Proper citation: JASPAR (RRID:SCR_003030) Copy   

•   Source: SciCrunch Registry

http://www.qgene.org/

A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.

Proper citation: QGene (RRID:SCR_003209) Copy   

•   Source: SciCrunch Registry

http://www.humanconnectomeproject.org/

A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

Proper citation: MGH-USC Human Connectome Project (RRID:SCR_003490) Copy   

•   Source: SciCrunch Registry

https://www.hsph.harvard.edu/alkes-price/software/

Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software)

Proper citation: Hapmix (RRID:SCR_004203) Copy   

•   Source: SciCrunch Registry

https://pathoman.mskcc.org/

Web application to automate germline genomic variant curation from clinical sequencing based on ACMG guidelines. Aggregates multiple tracks of genomic, protein and disease specific information from public sources.

Proper citation: PathoMAN (RRID:SCR_026552) Copy   

•   Source: SciCrunch Registry

http://krunch.med.yale.edu/haplo/

Software application that estimates frequencies of multi-site haplotypes using the EM algorithm (entry from Genetic Analysis Software)

Proper citation: HAPLO 2 (RRID:SCR_009059) Copy   

•   Source: SciCrunch Registry

https://dsgweb.wustl.edu/aldi/software/manuals/unphased/Unphased_manual.pdf

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A suite of programs for association analysis of multilocus haplotypes from unphased genotype data. These include TDTPHASE for case-parent trios, COCAPHASE for case/control data, QTPHASE for quantitative traits in unrelateds, PDTPHASE for general pedigrees, and QPDTPHASE for quantitative traits in general pedigrees. Features include global and individual haplotype tests, main effects and conditional tests, grouping of rare haplotypes, pairwise comparisons of haplotype risk, flexible permutation procedures and calculation of LD measures.

Proper citation: UNPHASED (RRID:SCR_009056) Copy   

•   Source: SciCrunch Registry

http://dceg.cancer.gov/tools/design/power

Windows-based program for computation of sample size and power for binary outcome studies (case-control and cohort studies) based on a logistic-like regression model with one covariate or two covariates (e.g., gene-exposure interactions). (entry from Genetic Analysis Software)

Proper citation: POWER (RRID:SCR_009057) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~mcpeek/software/dhsmap/

Software application for fine-mapping of qualitative traits by linkage disequilibrium. Given a set of marker haplotypes or genotypes from affected individuals, haplotypes or genotypes from appropriately selected controls, and a genetic map of the markers at which both sets of individuals are typed, DHSMAP estimates the location of the trait-associated variant by maximum likelihood or maximum quasi-likelihood. (entry from Genetic Analysis Software)

Proper citation: DHSMAP (RRID:SCR_009160) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/amelia/

Software application that employs allele matching to analyse the effects of rare variants within a specific locus. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, AMELIA has been developed as an allele-matching approach that is robust to the presence of both directions of effect for variants within the locus analysed. (entry from Genetic Analysis Software)

Proper citation: AMELIA (RRID:SCR_009119) Copy   

•   Source: SciCrunch Registry

http://www.decode.com/software/

Software application that is a faster version of GENEHUNTER and Allegro 1.2 (several degrees of increase of speed, can handle bigger families, up to 50 bits) (entry from Genetic Analysis Software)

Proper citation: ALLEGRO (RRID:SCR_009116) Copy   

•   Source: SciCrunch Registry

http://www.imbs.uni-luebeck.de/pub/sibsim/index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that simulates either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scalable way. It is based on XML, completely written in C++ and published under the GNU General Public License.

Proper citation: SIBSIM (RRID:SCR_009113) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/IGG.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: IGG (RRID:SCR_009114) Copy   

•   Source: SciCrunch Registry

http://ibi.zju.edu.cn/software/qtlnetwork

Software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines. (entry from Genetic Analysis Software)

Proper citation: QTLNETWORK (RRID:SCR_009078) Copy   

•   Source: SciCrunch Registry

http://pritch.bsd.uchicago.edu/treeld.html

Free software tool for mapping complex trait loci. TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data. (entry from Genetic Analysis Software)

Proper citation: TREELD (RRID:SCR_009111) Copy   

•   Source: SciCrunch Registry

http://www.hsph.harvard.edu/faculty/alkes-price/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application using a method for combining SNP association and admixture association statistics to increase power in GWAS in admixed populations. (entry from Genetic Analysis Software)

Proper citation: MIXSCORE (RRID:SCR_009076) Copy   

•   Source: SciCrunch Registry

http://www.twin-research.ac.uk/WebPowQ/PowQ.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A user-friendly, graphical package for power evaluation and enhancement planning through variance component linkage analysis in a multipoint framework. (entry from Genetic Analysis Software)

Proper citation: POWQ (RRID:SCR_009077) Copy   

•   Source: SciCrunch Registry

http://pritchardlab.stanford.edu/software.html

Software application that is a companion program to STRUCTURE that is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure. (entry from Genetic Analysis Software)

Proper citation: STRAT (RRID:SCR_009110) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/u/prastas/haplovisual/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOVISUAL (RRID:SCR_009073) Copy   

•   Source: SciCrunch Registry