├── .Rbuildignore ├── .Rinstignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── csq.R ├── es.R ├── import_OpenGWAS.R ├── import_eQTLCatalogue.R ├── novelty_check.R ├── pQTLtools.R ├── pav.r ├── peptideAssociationPlot.R ├── phenoscanner.R ├── pqtlMR.R ├── qtl_lookup.R ├── run_TwoSampleMR.R ├── run_coloc.R ├── turboman.r ├── turboqq.r └── uniprot2ids.R ├── README.Rmd ├── README.md ├── data ├── datalist └── protein_altering_variants.rda ├── docs ├── .nojekyll ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── LocusZoom.js.html │ ├── LocusZoom.js_files │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── darkly.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── jquery-3.6.0 │ │ │ ├── jquery-3.6.0.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ └── jquery-3.6.0.min.map │ │ ├── jqueryui-1.13.2 │ │ │ ├── AUTHORS.txt │ │ │ ├── LICENSE.txt │ │ │ ├── images │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ ├── index.html │ │ │ ├── jquery-ui.css │ │ │ ├── jquery-ui.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.css │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.css │ │ │ └── jquery-ui.theme.min.css │ │ ├── navigation-1.1 │ │ │ ├── codefolding-lua.css │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ │ └── tocify-1.9.1 │ │ │ ├── jquery.tocify.css │ │ │ └── jquery.tocify.js │ ├── SCALLOP-Caprion.html │ ├── SCALLOP-Caprion_files │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── darkly.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── jquery-3.6.0 │ │ │ ├── jquery-3.6.0.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ └── jquery-3.6.0.min.map │ │ ├── jqueryui-1.13.2 │ │ │ ├── AUTHORS.txt │ │ │ ├── LICENSE.txt │ │ │ ├── images │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ ├── index.html │ │ │ ├── jquery-ui.css │ │ │ ├── jquery-ui.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.css │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.css │ │ │ └── jquery-ui.theme.min.css │ │ ├── navigation-1.1 │ │ │ ├── codefolding-lua.css │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ │ └── tocify-1.9.1 │ │ │ ├── jquery.tocify.css │ │ │ └── jquery.tocify.js │ ├── SF-pQTL-GWAS.png │ ├── bioconductor.html │ ├── bioconductor │ │ ├── ComBat-1.png │ │ ├── ComBat-2.png │ │ ├── ComBat-3.png │ │ ├── ComBat-4.png │ │ ├── DESeq2-1.png │ │ ├── GeneNet-1.png │ │ ├── GeneNet-2.png │ │ ├── GeneNet-3.png │ │ ├── a1bg-1.png │ │ ├── heatmap-1.png │ │ ├── lod-1.png │ │ ├── mcpca-1.png │ │ ├── plots-1.png │ │ ├── plots-2.png │ │ ├── quantro-1.png │ │ ├── quantro-2.png │ │ └── test-1.png │ ├── bioconductor_files │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── darkly.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── jquery-3.6.0 │ │ │ ├── jquery-3.6.0.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ └── jquery-3.6.0.min.map │ │ ├── jqueryui-1.13.2 │ │ │ ├── AUTHORS.txt │ │ │ ├── LICENSE.txt │ │ │ ├── images │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ ├── index.html │ │ │ ├── jquery-ui.css │ │ │ ├── jquery-ui.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.css │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.css │ │ │ └── jquery-ui.theme.min.css │ │ ├── navigation-1.1 │ │ │ ├── codefolding-lua.css │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ │ └── tocify-1.9.1 │ │ │ ├── jquery.tocify.css │ │ │ └── jquery.tocify.js │ ├── dag.svg │ ├── data │ │ ├── A1BG-rs145685027.json │ │ ├── ACE-rs4353.json │ │ ├── datalist │ │ ├── protein_altering_variants.rda │ │ └── top_hits.json │ ├── esse.html │ ├── esse │ │ ├── lod-1.png │ │ ├── mcpca-1.png │ │ ├── plots-1.png │ │ ├── plots-2.png │ │ └── test-1.png │ ├── esse_files │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── darkly.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── jquery-3.6.0 │ │ │ ├── jquery-3.6.0.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ └── jquery-3.6.0.min.map │ │ ├── jqueryui-1.13.2 │ │ │ ├── AUTHORS.txt │ │ │ ├── LICENSE.txt │ │ │ ├── images │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ ├── index.html │ │ │ ├── jquery-ui.css │ │ │ ├── jquery-ui.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.css │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.css │ │ │ └── jquery-ui.theme.min.css │ │ ├── navigation-1.1 │ │ │ ├── codefolding-lua.css │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ │ └── tocify-1.9.1 │ │ │ ├── jquery.tocify.css │ │ │ └── jquery.tocify.js │ ├── fig2d.html │ ├── fig3d.html │ ├── heatmaply.html │ ├── index.html │ ├── lz.html │ ├── mcpca3d.html │ ├── pQTLtools.html │ ├── pQTLtools │ │ ├── GREAT-1.png │ │ ├── GREAT-2.png │ │ ├── TwoSampleMR-1.png │ │ ├── TwoSampleMR-2.png │ │ ├── TwoSampleMR-3.png │ │ ├── TwoSampleMR-4.png │ │ ├── ctbar-1.png │ │ ├── ctcircos-1.png │ │ ├── forest-1.png │ │ ├── forest-2.png │ │ ├── forest-3.png │ │ ├── forest-4.png │ │ ├── karyoplot-1.png │ │ ├── mr-1.png │ │ ├── pQTLs-1.png │ │ ├── pqtlMR-1.png │ │ ├── qtl2dplot-1.png │ │ └── sh2b3-1.png │ ├── pQTLtools_files │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── darkly.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── jquery-3.6.0 │ │ │ ├── jquery-3.6.0.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ └── jquery-3.6.0.min.map │ │ ├── jqueryui-1.13.2 │ │ │ ├── AUTHORS.txt │ │ │ ├── LICENSE.txt │ │ │ ├── images │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ ├── index.html │ │ │ ├── jquery-ui.css │ │ │ ├── jquery-ui.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.css │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.css │ │ │ └── jquery-ui.theme.min.css │ │ ├── navigation-1.1 │ │ │ ├── codefolding-lua.css │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ │ └── tocify-1.9.1 │ │ │ ├── jquery.tocify.css │ │ │ └── jquery.tocify.js │ ├── rulegraph.svg │ ├── snakemake.html │ ├── snakemake_files │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── darkly.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── jquery-3.6.0 │ │ │ ├── jquery-3.6.0.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ └── jquery-3.6.0.min.map │ │ ├── jqueryui-1.13.2 │ │ │ ├── AUTHORS.txt │ │ │ ├── LICENSE.txt │ │ │ ├── images │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ ├── index.html │ │ │ ├── jquery-ui.css │ │ │ ├── jquery-ui.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.css │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.css │ │ │ └── jquery-ui.theme.min.css │ │ ├── navigation-1.1 │ │ │ ├── codefolding-lua.css │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ │ └── tocify-1.9.1 │ │ │ ├── jquery.tocify.css │ │ │ └── jquery.tocify.js │ ├── spectrum.html │ ├── spectrum │ │ └── a1bg-1.png │ ├── spectrum_files │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── darkly.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── jquery-3.6.0 │ │ │ ├── jquery-3.6.0.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ └── jquery-3.6.0.min.map │ │ ├── jqueryui-1.13.2 │ │ │ ├── AUTHORS.txt │ │ │ ├── LICENSE.txt │ │ │ ├── images │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ ├── index.html │ │ │ ├── jquery-ui.css │ │ │ ├── jquery-ui.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.css │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.css │ │ │ └── jquery-ui.theme.min.css │ │ ├── navigation-1.1 │ │ │ ├── codefolding-lua.css │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ │ └── tocify-1.9.1 │ │ │ ├── jquery.tocify.css │ │ │ └── jquery.tocify.js │ └── stack.html ├── authors.html ├── deps │ ├── MathJax-3.2.2 │ │ └── tex-chtml.min.js │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.5.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── logo.svg ├── news │ └── index.html ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── blank_plot.html │ ├── clump_data.args.html │ ├── csq.html │ ├── extract_outcome_data.args.html │ ├── figures │ │ ├── ceu.svg │ │ └── logo.svg │ ├── format_data.args.html │ ├── genequeries.html │ ├── get.prop.below.LLOD-1.png │ ├── get.prop.below.LLOD.html │ ├── harmonise_data.args.html │ ├── import_OpenGWAS.html │ ├── import_eQTLCatalogue.html │ ├── index.html │ ├── make_ExpressionSet-1.png │ ├── make_ExpressionSet-10.png │ ├── make_ExpressionSet-11.png │ ├── make_ExpressionSet-12.png │ ├── make_ExpressionSet-13.png │ ├── make_ExpressionSet-14.png │ ├── make_ExpressionSet-15.png │ ├── make_ExpressionSet-16.png │ ├── make_ExpressionSet-17.png │ ├── make_ExpressionSet-18.png │ ├── make_ExpressionSet-19.png │ ├── make_ExpressionSet-2.png │ ├── make_ExpressionSet-20.png │ ├── make_ExpressionSet-21.png │ ├── make_ExpressionSet-22.png │ ├── make_ExpressionSet-23.png │ ├── make_ExpressionSet-24.png │ ├── make_ExpressionSet-25.png │ ├── make_ExpressionSet-26.png │ ├── make_ExpressionSet-3.png │ ├── make_ExpressionSet-4.png │ ├── make_ExpressionSet-5.png │ ├── make_ExpressionSet-6.png │ ├── make_ExpressionSet-7.png │ ├── make_ExpressionSet-8.png │ ├── make_ExpressionSet-9.png │ ├── make_ExpressionSet.html │ ├── mr_forest_plot2.html │ ├── mr_funnel_plot2.html │ ├── mr_leaveoneout_plot2.html │ ├── mr_scatter_plot2.html │ ├── novelty_check.html │ ├── pQTLtools-package.html │ ├── pQTLtools.html │ ├── peptideAssociationPlot.html │ ├── peptideMapping.html │ ├── pqtlMR.html │ ├── protein_altering_variants.html │ ├── qtl_lookup.html │ ├── regionqueries.html │ ├── run_TwoSampleMR-1.png │ ├── run_TwoSampleMR-2.png │ ├── run_TwoSampleMR-3.png │ ├── run_TwoSampleMR-4.png │ ├── run_TwoSampleMR.html │ ├── run_coloc.html │ ├── snpqueries.html │ ├── swap.html │ ├── turboman.html │ ├── turboqq.html │ └── uniprot2ids.html ├── search.json └── sitemap.xml ├── inst ├── PPI │ └── README.md ├── README.md ├── REFERENCES.bib ├── STRING │ └── change_STRING_colors.py ├── UniProt │ ├── README.md │ ├── accession.py │ ├── gene.py │ └── uniprot2ids.py ├── eQTL-Catalogue │ ├── column_names.Alasoo │ ├── column_names.CEDAR │ ├── column_names.GTEx │ ├── hg19ToHg38.over.chain │ ├── tabix_ftp_paths.tsv │ ├── tabix_ftp_paths_ge.tsv │ └── tabix_ftp_paths_gtex.tsv ├── scripts │ ├── cran.sh │ └── docs.sh ├── snakemake │ ├── LICENSE │ ├── config.yaml │ ├── input │ │ ├── MR.csv │ │ ├── Obs_HF.csv │ │ ├── Obs_HF2.csv │ │ └── ld │ │ │ ├── CD40.ld │ │ │ ├── CD40.snplist │ │ │ ├── OPG.ld │ │ │ └── OPG.snplist │ └── workflow │ │ ├── Snakefile │ │ ├── envs │ │ └── conda.yaml │ │ ├── r │ │ ├── MR_analysis.R │ │ ├── MR_functions.R │ │ └── Obs_analysis.R │ │ └── report │ │ └── workflow.rst ├── tests │ ├── IL.12B.txt │ ├── INF1.METAL │ ├── INF1.merge │ ├── Ins.csv │ ├── MMP.10-cis.mrx │ ├── OPG-rs2247769.RDS │ ├── Out.csv │ ├── PROC.rda │ ├── README.md │ ├── UKB-PPP.txt │ ├── annot.RDS │ ├── efo.txt │ ├── hgnc.rda │ ├── inf1.tmp │ ├── novel_data.rda │ └── pQTL_genes.txt └── turboman │ ├── README.Rmd │ ├── README.md │ ├── turboman_hg19_reference_data.rda │ └── turboman_hg38_reference_data.rda ├── man ├── blank_plot.Rd ├── clump_data.args.Rd ├── csq.Rd ├── extract_outcome_data.args.Rd ├── figures │ ├── ceu.svg │ └── logo.svg ├── format_data.args.Rd ├── genequeries.Rd ├── get.prop.below.LLOD.Rd ├── harmonise_data.args.Rd ├── import_OpenGWAS.Rd ├── import_eQTLCatalogue.Rd ├── make_ExpressionSet.Rd ├── mr_forest_plot2.Rd ├── mr_funnel_plot2.Rd ├── mr_leaveoneout_plot2.Rd ├── mr_scatter_plot2.Rd ├── novelty_check.Rd ├── pQTLtools.Rd ├── peptideAssociationPlot.Rd ├── peptideMapping.Rd ├── pqtlMR.Rd ├── protein_altering_variants.Rd ├── qtl_lookup.Rd ├── regionqueries.Rd ├── run_TwoSampleMR.Rd ├── run_coloc.Rd ├── snpqueries.Rd ├── swap.Rd ├── turboman.Rd ├── turboqq.Rd └── uniprot2ids.Rd ├── pkgdown ├── _pkgdown.yml └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico └── vignettes ├── LocusZoom.js.Rmd ├── SF-pQTL-GWAS.png ├── bioconductor.Rmd ├── dag.svg ├── data ├── A1BG-rs145685027.json ├── ACE-rs4353.json └── top_hits.json ├── lz.html ├── nature-genetics.csl ├── pQTLtools.Rmd ├── rulegraph.svg ├── snakemake.Rmd 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