New Features in Version 2.9

  • Detailed Allele Download
  • We implemented a new feature in the Detailed SNP view, which allows the download of allele specific information about a certain SNP. The CSV file contains the sample id, its allele and the phenotypic value.

    In addition a variety of bug fixes and performance updates had been deployed.

    New Features in Version 2.8

  • We added a Representational State Transfer (REST) API to easyGWAS.

    This allows users to obtain information from easyGWAS in various forms, simply by using URLs. An example of a REST query is to get all meta-information (e.g. latitude, longitude, and others) of a particular sample.

    For example to access meta-information for a sample with id 6944

    For example to access all public phenotypes

    New Features in Version 2.7

  • Enhancement of Variant Annotations
  • We extended the variant annotation pipeline of easyGWAS.

    Variants are now also annotated with variant effect predictions from Variant Effect Predictor (VEP).

    Therefore, easyGWAS uses the public REST API

    We extended the "Detailed SNP" view. You can access this view by clicking on any SNP in the Manhattan plot or the LD plot in the "Detailed SNP" view.

    You can access a demo of the "Detailed SNP" view here: Demo

    In addition, we have updated the "SNP Annotation" view. Here, we now added a button which redirects every user to the "Detailed SNP" view for a SNP of interest.

    New Features in Version 2.6

  • AraPheno Import Support
  • We extended easyGWAS to allow the import of publically available phenotypes from AraPheno.

    AraPheno is a central repository for population scale phenotype data for the model plant Arabidopsis thaliana

    New Features in Version 2.5

  • Detailed SNP View
  • Detailed information about the allele distrbution and its phenotypic values is shown, as well as dynamic linkage disequilibrium plots.

    If available, gene annotations are shown in the LD plot.

    Click here to see a live example: Demo

  • Comparison of GWAS Across and Within Datasets
  • User now can compare the results between public and private GWAS!

    A live Demo can be found here: Live Demo

    Pairwise Comparison of GWAS

    Pairwise comparison of genome-wide association study results. All plots are dynamic. Users can hover with their mouse over any dot in the correlation map at the left. All other plots are automatically updated correspondingly.

    The correlation map on the left shows all correlations between the phenotypes used for the individual GWAS.

    The phenotype-phenotype scatter plot on the right shows all phenotypic values of phenotype x against all phenotypic values of phenotype y.

    The sample overlap plot on the right shows the overlap of samples between the samples of GWAS x and GWAS y.

    The phenotype-phenotype manhattan plot at the buttom shows the top 1000 association results of GWAS x and GWAS y.

    Shared Associations between GWAS

    The "Shared Associations" tab shows the top x SNPs for each GWAS experiment.

    SNPs that can be found to be associated between different GWAS experiments are linked to each other.

    Filled circles are significantly associated SNPs, whereas empty circles are not significantly associated.

  • Upload of Custom Gene Annotation Sets
  • User now can upload custom gene annotation sets for public and private species.

  • Others
  • Several performance adjustments and bugfixes.