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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://www.bio.unc.edu/faculty/vision/lab/mappop/

Software application that selects high resolution mapping subsamples and performs bin mapping (entry from Genetic Analysis Software)

Proper citation: MAPPOP (RRID:SCR_013490) 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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http://genome.crg.es/GOToolBox/

The GOToolBox web server provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. The web version of the GOToolBox is free for non-commercial users only. Users from commercial companies are allowed to use the site during a reasonable testing period. For a regular use of the web version, a license fee should be paid. We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license. Platform: Online tool

Proper citation: GOToolBox Functional Investigation of Gene Datasets (RRID:SCR_003192) Copy   

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https://reich.hms.harvard.edu/software

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.

Proper citation: Ancestrymap (RRID:SCR_004353) Copy   

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http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer/

A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region.

Proper citation: CandiSNPer (RRID:SCR_005173) Copy   

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http://clinicaltrials.gov/show/NCT01211678

A consortium evaluating a new biomarker screening test that might help identify patients with rheumatoid arthritis (RA) who are unlikely to benefit from anti-tumor necrosis factor-alpha (TNFalpha) medications. BATTER-UP will enroll around 1,000 patients being treated by one of several marketed anti-TNF RA drugs: Enbrel, Remicade, Humira, Simponi, or Cimzia. Through data analyses and predictive response modeling, the consortium aims to better understand which patients with RA will derive the greatest benefit from TNF inhibitors. The investigators in this observational study will attempt to validate an 8-gene biomarker set based on work by Biogen Idec researchers as likely to predict anti-TNF responsiveness in patients with RA. In preliminary results, the 8-gene biomarker set predicted with 89% accuracy individuals who did not reach European League Against Rheumatism (EULAR) Disease Activity Score (DAS)-28 good response after 14 weeks of treatment. The 8 genes included in the screen are CLTB, MXRA7, CXorf52, COL4A3BP, YIPF6, FAM44A, SFRS2, and PGK1. Biological samples and clinical outcome information will be used to confirm and extend the utility of previously published biomarkers that can predict response to anti-TNF agents. These data may also generate new hypotheses for further testing. The BATTER-UP samples and data will be established as a reference set for investigation of personalized medicine in RA. The study will be a resource of DNA and other biological materials that can be investigated for biomarkers in the future as new technologies arise.

Proper citation: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations (RRID:SCR_004019) Copy   

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https://niaid.github.io/dcas/

Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: dCAS (RRID:SCR_016612) Copy   

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http://www.genetherapyreview.com/gene-therapy-research

The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.

Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy   

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http://nt-salkoff.wustl.edu/portal/hgxpp001.aspx?2

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Supplies potassium channel cDNA clones in vectors suitable for functional expression and stocks of gene knockout strains. Supporting this resource base are studies showing the basic biophysical properties of the channels, studies showing the phenotypes of mutants, and information on the cell-type expression patterns of potassium channels. Studies of potassium channel cell-type expression patterns and functional properties; studies of behavioral phenotypes; generation of knockout mutants. Full-length cDNAs encoding C. elegans potassium channels in a vector suitable for functional expression in Xenopus oocytes and mammalian cell lines are available on request. Information is also provided describing the cell-type expression patterns and basic biophysical properties of potassium channels. And data on behavioral phenotypes are also available. C. elegans strains carrying knockouts of potassium channels are also generated and deposited at the C. elegans stock center at the University of Minnesota.

Proper citation: A Comprehensive Resource Base for C. elegans K+ Channels (RRID:SCR_008360) Copy   

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http://bioafrica.mrc.ac.za/index.html

The BioAfrica HIV-1 Proteomics Resource is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. HIV Proteomics Resource contains information about each HIV-1 gene product in regard to expression, post-transcriptional / post-translational modifications, localization, functional activities, and potential interactions with viral and host macromolecules. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites.

Proper citation: BioAfrica HIV Informatics in Africa (RRID:SCR_002295) Copy   

•   Source: SciCrunch Registry

http://cgap.nci.nih.gov/

Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools

Proper citation: Cancer Genome Anatomy Project (RRID:SCR_003072) Copy   

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http://www.well.ox.ac.uk/happy/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).

Proper citation: Happy (RRID:SCR_001395) Copy   

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http://www.biomed.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This laboratory facilities contain core research space for monoclonal antibody production, oligonucleotide and peptide synthesis, gene cloning, DNA sequencing, high performance liquid chromatography, tissue culture, positron emission tomography, magnetic resonance spectroscopy and electron microscopy.

Proper citation: The Biomedical Research Foundation - Current Research (RRID:SCR_001564) Copy   

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https://www.hgsc.bcm.edu/content/sea-urchin-genome-project

Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology.

Proper citation: Sea Urchin Genome Project (RRID:SCR_001735) Copy   

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http://www-genome.stanford.edu/

This resource hyperlinks to systematic analysis projects, resources, laboratories, and departments at Stanford University.

Proper citation: Stanford Genomic Resourses (RRID:SCR_001874) Copy   

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http://www.oege.org/

Portal for researchers to locate information relevant to interpretation and follow-up of human genetic epidemiological discoveries, including: a range of population and case and family genetic epidemiological studies, relevant gene and sequence databases, genetic variation databases, trait measurement, resource labs, journals, software, general information, disease genes and genetic diversity.

Proper citation: Online Encyclopedia for Genetic Epidemiology studies (RRID:SCR_001825) 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   

•   Source: SciCrunch Registry