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vignettes/gwas2020.Rmd

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%\VignetteEncoding{UTF-8}
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---
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This document details changes and new features specifically relating to the TwoSampleMR R package and the GWAS database behind it.
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This document details changes and new features specifically relating to the TwoSampleMR R package and the IEU OpenGWAS database behind it.
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## What has changed
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### Authentication
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Previously you would automatically be asked to authenticate any query to the database, through google. Now, we are making authentication voluntary - something that you do at the start of a session only if you need access to specific private datasets on the database. For the vast majority of use cases this is not required.
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Previously you would automatically be asked to authenticate any query to the database, through Google. Now, we are making authentication voluntary - something that you do at the start of a session only if you need access to specific private datasets on the database. For the vast majority of use cases this is not required.
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Another change is that the R package that managed the authentication has updated, and the file tokens generated are slightly different. For full information on how to deal with this, see here: https://mrcieu.github.io/ieugwasr/articles/guide.html#authentication
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## Key links
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- The IEU GWAS database: https://gwas.mrcieu.ac.uk
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- API to the IEU GWAS database: https://api.opengwas.io/api/
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- The IEU OpenGWAS database: https://gwas.mrcieu.ac.uk
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- API to the IEU OpenGWAS database: https://api.opengwas.io/api/
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- ieugwasr package, for R access to the API: https://mrcieu.github.io/ieugwasr/
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- ieugwaspy package, for python access to the API: https://github.com/MRCIEU/ieugwaspy/ (Under construction)
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- ieugwaspy package, for python access to the API: https://github.com/MRCIEU/ieugwaspy/
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- gwasvcf package, R interface to GWAS VCF files: https://mrcieu.github.io/gwasvcf/
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- pygwasvcf package, python interface to GWAS VCF files: https://github.com/mrcieu/pygwasvcf (Under construction)
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- gwasglue package, linking GWAS data to various analytical methods: https://mrcieu.github.io/gwasglue/ (Functional, under construction)
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- pygwasvcf package, python interface to GWAS VCF files: https://github.com/mrcieu/pygwasvcf
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- gwasglue package, linking GWAS data to various analytical methods: https://mrcieu.github.io/gwasglue/
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- gwas2vcf online tool, allowing users to create GWAS VCF files from summary data: https://github.com/MRCIEU/gwas2vcf
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## How to request new data

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