A platform for Mendelian randomisation & PheWAS using results from GWAS. Includes API, web interface and R packages elifesciences.org/articles/3…
Joined October 2016
- Tweets 110
- Following 22
- Followers 653
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Photos and videos
Great thread on MR-Base! includes description of my recent updates x.com/Prime2/status/10018974…
30 May 2018
We describe the design and scope of @mrbase2 (mrbase.org): a platform that integrates a database of complete GWAS results (no restrictions according to p-values) with an API, webapp and R packages that automate Mendelian randomization (MR) using GWAS results 2/n
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MR-Base retweeted
7 Jul 2021
New postdoc opportunity in Health Data Science at the MRC Integrative Epidemiology Unit (@mrcieu) at University of Bristol. Get in touch if interested! bristol.ac.uk/jobs/find/deta…
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MR-Base retweeted
24 Feb 2021
Join me at #ElasticCC where I'll be talking about how we use Elasticsearch for @OpenGwas. This is @Elastic’s free technical event from the community, for the community — happening from Feb 26 - 27 ela.st/community-conference
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We've made some major changes to mrbase and the twosamplemr R package. Details here: mrcieu.github.io/TwoSampleMR…
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Were experiencing problems with the mrbase web app at the moment. You can continue to access the data via github.com/MRCIEU/TwoSampleM… and @OpenGwas while we work on a fix
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Analytical tools - The gwasglue R package connects the local or cloud data sources, as well as cloud hosted LD reference panels, to a range of third party tools. Fine mapping, colocalisation, MR, genetic correlations, PheWAS, etc. mrcieu.github.io/gwasglue/
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Local querying - All the data can also be downloaded as GWAS VCF files. There is a need for a storage format that is unambiguous, self contained and performant for querying. We designed this for large scale analysis on compute clusters bit.ly/33VbOfL
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Cloud querying - elasticsearch to store the data, hosted in collaboration with Oracle Cloud Infrastructure. We worked hard to optimise queries, allowing rapid search by position, rsid, range, p-value. This can be done in R, python or through a RESTful API.
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QC process - we align the non-effect allele to the human genome reference sequence; and annotate the positions with dbSNP identifiers. Example QC report: gwas.mrcieu.ac.uk/datasets/u…
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OpenGWAS (gwas.mrcieu.ac.uk/) is a harmonised database of complete GWAS summary data (126 billion associations, almost 15000 complete datasets) with programmatic connections to a range of third party analytical tools.
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Continued data harvesting - for new GWAS results that are published, upload them to the EBI GWAS catalog and we will pull them in from there. For unpublished results, or large batches, we have pipelines to do that. Get in touch here: github.com/mrcieu/opengwas-r…
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Huge thanks to @The_MRC, @OracleCloud and @wellcometrust for funding much of this, and team (@explodecomputer @tomrgaunt @elswob @matt_s_lyon @prime2 @assetweb @JonJHallett and others) for making a hopefully useful community resource
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We built the OpenGWAS resource to be a free and open platform to support work on GWAS summary data. Much of it is based on extensive feedback on @mrbase2 from both internal and external colleagues. Paper here: bit.ly/2DRbHGT, key points below:
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MR-Base retweeted
31 May 2020
Paper from Matt Lyon @mrc_ieu describing an adapted variant call format (VCF) for efficient and robust storage of GWAS summary statistics disq.us/t/3p55pl6
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MR-Base retweeted
11 May 2020
Our multi-omics study of COVID-19 drug targets are online now 😃
medrxiv.org/content/10.1101/…
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MR-Base retweeted
28 Apr 2020
EpiGraphDB v0.3.0 is released today, with ~10x expansion of data to support #triangulation of #epidemiology evidence and #datamining.
Check out the latest and greatest features at epigraphdb.org/!
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MR-Base retweeted
26 Nov 2019
Guidelines on performing Mendelian randomization investigations written by an all-star line-up of MR researchers are now available on Wellcome Open Research: wellcomeopenresearch.org/art… - represents a consensus statement after 12 months of deliberation. Comments welcome!
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MR-Base retweeted
4 Jul 2019
The @mrc_ieu GWAS database is now being hosted on Oracle Cloud. Should see some major performance improvements. Access it now via @mrbase2 and github.com/MRCIEU/TwoSampleM…. Big thanks to @OracleCloud and @philrbates
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MR-Base retweeted
6 May 2019
Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases biorxiv.org/content/10.1101/…
New MR paper suggest proteins with MR and colocalization evidence is more likely to predict drug trial success
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