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    GWASrap

Cite this (GWASrap, RRID:SCR_013144)

URL: http://jjwanglab.org/gwasrap

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, data set, web service, service resource, software resource, data or information resource

GWASrap is a comprehensive web-based bioinformatics tool to systematically support variant representation, annotation and prioritization for data generated from genome-wide association studies (GWAS) and Next Generation Sequencing (NGS). Our web-based framework utilizes state-of-the-art web technologies to maximize user interaction and visualization of the results. For a given SNP dataset with its P-values, GWASrap will first provide a Circos-style plot to visualize any genetic variants at either the genome or chromosome level. The tool then combines different genomic features (SNP/CNV density, disease susceptibility loci, etc.) with comprehensive annotations that give the researcher an intuitive view of the functional significance of the different genomic regions. The detailed statistics of the underlying study are also displayed on the web page, including variant distribution in different functional categories, classic Manhattan plot and QQ plot. Users can perform interactive operations in the Manhattan panel, such as zooming in and out to search regions or markers of interest. The system can also display a comprehensive range of relevant information from variant genetic attributes to nearby genomic elements, such as enhancers or non-coding RNAs. Furthermore, researchers can obtain extensive functional predictions for various features including transcription factor-binding sites, miRNA and miRNA target sites, and their predicted changes caused by the genetic variants. Our system can re-prioritize genetic variants by combining the original statistical value and variant prioritization score based on a simple additive effect equation. Researchers can also re-evaluate the significance of a trait/disease-associated SNP (TAS) using the dynamic linkage disequilibrium (LD) panel or the tree-like network panel. The GWASrap supports input variants in different formats, not only common variants with a dbSNP rs ID but also rare variants from NGS data, which are represented by chromosome and locations. GWASrap provides a range of web services for data retrieving about the annotation information and effect prediction of each variant in dbSNP using the SOAP interface. The WSDL for each service is available in the API tab. Each service returns JSON string including all related information with key/value. GWASrap provides running results about some current published GWAS as well as a category view for each hot disease / trait. The dataset is brought from published database GWAS or curated from literature.

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Cite this (NIMH Center for Collaborative Genetic Studies on Mental Disorders, RRID:SCR_006698)

URL: https://www.nimhgenetics.org/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, biomaterial supply resource, material service resource, data set, service resource, cell repository, material resource, biomaterial manufacture, data or information resource

A center that produces, stores, and distributes the clinical data and biomaterials (DNA samples and cell lines) that are available from the NIMH Human Genetics Initiative. The Center creates and distributes computational tools that support investigation and analysis of the clinical data, along with tools that enable researchers to determine which samples or data might be of use to them, so that they may request access from NIMH. The goal of this Initiative is to study individuals affected with schizophrenia, bipolar disorder, or Alzheimer's disease and their relatives, in order to establish a national resource of clinical/diagnostic information and immortalized cell lines for DNA extraction. Data is available from diagnostic and family interviews for genetic studies.

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