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<h1 class="title toc-ignore">Enrichment results of high-density lipoprotein</h1>
<h4 class="author"><em>Xiang Zhu</em></h4>
<h4 class="date"><em>2017-04-12</em></h4>
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<p><strong>Last updated:</strong> 2018-10-05</p>
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<div id="input-data" class="section level2">
<h2>Input data</h2>
<p>Results below were generated from the GWAS summary statistics published in the paper <a href="https://www.ncbi.nlm.nih.gov/pubmed/20686565">“Biological, Clinical and Population Relevance of 95 Loci for Blood Lipids” (<em>Nature</em>, 2010)</a>. The summary data file is available at <a href="http://csg.sph.umich.edu/willer/public/lipids2010" class="uri">http://csg.sph.umich.edu/willer/public/lipids2010</a>.</p>
</div>
<div id="analysis-results" class="section level2">
<h2>Analysis results</h2>
<p>Enrichment analyses are summarized by the following three quantities.</p>
<ul>
<li><strong>BF:</strong> Bayes factor comparing the enrichment model against the baseline model;</li>
<li><strong>Outside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “outside” the gene set;</li>
<li><strong>Inside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “inside” the gene set.</li>
</ul>
<p>The first quantity reflects the significance of enrichment, whereas the last two capture the magnitude of enrichment. For each gene set, we report these three quantities in the last three columns of tables below, on log 10 scale.</p>
<div id="biological-pathways" class="section level3">
<h3>Biological pathways</h3>
<div id="htmlwidget-983860bb2d7d6ad3a872" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-983860bb2d7d6ad3a872">{"x":{"filter":"none","data":[["Statin Pathway<br/>(2412, wiki, BioSystems)","Lipoprotein metabolism<br/>(2378, reactome, PC)","Lipid and lipoprotein metabolism<br/>(2961, reactome, PC)","Lipid digestion, mobilization, and transport<br/>(3093, reactome, BioSystems)","Exosome, archaea<br/>(484, kegg, BioSystems)","mRNA decay by 3' to 5' exoribonuclease<br/>(1254, reactome, PC)","KSRP destabilizes mRNA<br/>(1706, reactome, PC)","Role of Ran in mitotic spindle regulation<br/>(1168, biocarta, BioCarta)","Exosome, eukaryotes<br/>(1192, kegg, BioSystems)","HDL-mediated lipid transport<br/>(1555, reactome, PC)","Chylomicron-mediated lipid transport<br/>(1698, reactome, PC)","Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus<br/>(822, reactome, PC)","Gamma-carboxylation of protein precursors<br/>(915, reactome, PC)","Transcriptional activation of dbpb from mRNA<br/>(454, biocarta, BioCarta)","Removal of aminoterminal propeptides from gamma-carboxylated proteins<br/>(932, reactome, PC)","LDL endocytosis<br/>(673, reactome, PC)","Gamma-carboxylation, transport, and amino-terminal cleavage of proteins<br/>(1124, reactome, PC)","Triacylglyceride Synthesis<br/>(2097, wiki, BioSystems)","Vitamin B12 Metabolism<br/>(1860, wiki, BioSystems)","triacylglycerol degradation<br/>(1201, biocyc, BioSystems)","Cation-coupled Chloride cotransporters<br/>(792, reactome, PC)","Influenza Viral RNA Transcription and Replication<br/>(3638, reactome, PC)","Acylglycerol degradation<br/>(1290, kegg, BioSystems)","Influenza Viral RNA Transcription and Replication<br/>(3647, reactome, BioSystems)","Infectious disease<br/>(3900, reactome, BioSystems)","Influenza Life Cycle<br/>(3666, reactome, PC)","Influenza Life Cycle<br/>(3678, reactome, BioSystems)","Binding and Uptake of Ligands by Scavenger Receptors<br/>(2732, reactome, BioSystems)","Influenza Infection<br/>(3685, reactome, PC)","Binding and Uptake of Ligands by Scavenger Receptors<br/>(2742, reactome, PC)","Influenza Infection<br/>(3694, reactome, BioSystems)","Metabolism of RNA<br/>(3856, reactome, PC)","Triacylglycerol metabolism<br/>(76, panther, PC)","triacylglycerol degradation<br/>(1417, humancyc, PC)","PPAR signaling pathway<br/>(3239, kegg, BioSystems)","Fat digestion and absorption<br/>(2765, kegg, BioSystems)","Folate Metabolism<br/>(2138, wiki, BioSystems)","Role of PPAR-gamma Coactivators in Obesity and Thermogenesis<br/>(1071, biocarta, BioCarta)","Glycerolipid metabolism<br/>(3076, kegg, BioSystems)","HRD1/SEL1 ERAD complex<br/>(1446, kegg, BioSystems)","Low-density lipoprotein (LDL) pathway during atherogenesis<br/>(736, biocarta, BioCarta)","Host Interactions of HIV factors<br/>(3637, reactome, PC)","Host Interactions of HIV factors<br/>(3648, reactome, BioSystems)","ATF4 activates genes<br/>(2144, reactome, PC)","Visceral Fat Deposits and the Metabolic Syndrome<br/>(970, biocarta, BioCarta)","HIV Infection<br/>(3809, reactome, PC)","Retinoid metabolism and transport<br/>(2697, reactome, PC)","Retinoid metabolism and transport<br/>(2734, reactome, BioSystems)","HIV Infection<br/>(3814, reactome, BioSystems)","Selenium Pathway<br/>(3432, wiki, BioSystems)","Glycerolipid metabolism<br/>(1391, kegg, PC)","PERK regulates gene expression<br/>(2293, reactome, PC)","FXR and LXR Regulation of Cholesterol Metabolism<br/>(844, biocarta, BioCarta)","Antiviral mechanism by IFN-stimulated genes<br/>(3256, reactome, PC)","HIV Life Cycle<br/>(3680, reactome, PC)","ISG15 antiviral mechanism<br/>(3283, reactome, BioSystems)","Transport of Ribonucleoproteins into the Host Nucleus<br/>(2300, reactome, PC)","Nuclear import of Rev protein<br/>(2383, reactome, PC)","Fatty Acid Beta Oxidation<br/>(2542, wiki, BioSystems)","Nuclear import of Rev protein<br/>(2447, reactome, BioSystems)","HIV Life Cycle<br/>(3698, reactome, BioSystems)","NEP/NS2 Interacts with the Cellular Export Machinery<br/>(2290, reactome, PC)","Export of Viral Ribonucleoproteins from Nucleus<br/>(2371, reactome, PC)","Transport of Ribonucleoproteins into the Host Nucleus<br/>(2350, reactome, BioSystems)","Regulation of Glucokinase by Glucokinase Regulatory Protein<br/>(2297, reactome, PC)","Negative regulators of RIG-I/MDA5 signaling<br/>(2470, reactome, PC)","Vpr-mediated nuclear import of PICs<br/>(2392, reactome, PC)","NEP/NS2 Interacts with the Cellular Export Machinery<br/>(2349, reactome, BioSystems)","Export of Viral Ribonucleoproteins from Nucleus<br/>(2446, reactome, BioSystems)","Regulation of Glucokinase by Glucokinase Regulatory Protein<br/>(2344, reactome, BioSystems)","Transport of the SLBP independent Mature mRNA<br/>(2439, reactome, PC)","Interactions of Rev with host cellular proteins<br/>(2521, reactome, PC)","Interactions of Vpr with host cellular proteins<br/>(2427, reactome, PC)","Vpr-mediated nuclear import of PICs<br/>(2448, reactome, BioSystems)","Transport of the SLBP Dependant Mature mRNA<br/>(2481, reactome, PC)","Rev-mediated nuclear export of HIV RNA<br/>(2434, reactome, PC)","Orphan transporters<br/>(3498, reactome, PC)","Interactions of Rev with host cellular proteins<br/>(2574, reactome, BioSystems)","Transport of the SLBP independent Mature mRNA<br/>(2492, reactome, BioSystems)","Interactions of Vpr with host cellular proteins<br/>(2496, reactome, BioSystems)","Rev-mediated nuclear export of HIV RNA<br/>(2497, reactome, BioSystems)","Transport of the SLBP Dependant Mature mRNA<br/>(2535, reactome, BioSystems)","Transport of Mature mRNA Derived from an Intronless Transcript<br/>(2564, reactome, PC)","Nuclear Pore Complex (NPC) Disassembly<br/>(2472, reactome, PC)","Transport of Mature mRNAs Derived from Intronless Transcripts<br/>(2597, reactome, PC)","Transport of Mature mRNA Derived from an Intronless Transcript<br/>(2602, reactome, BioSystems)","Scavenging by Class B Receptors<br/>(567, reactome, PC)","Nuclear Pore Complex (NPC) Disassembly<br/>(2534, reactome, BioSystems)","Transport of Mature mRNAs Derived from Intronless Transcripts<br/>(2624, reactome, BioSystems)","Viral Messenger RNA Synthesis<br/>(2727, reactome, PC)","Late Phase of HIV Life Cycle<br/>(3635, reactome, PC)","Viral Messenger RNA Synthesis<br/>(2762, reactome, BioSystems)","Lysosome<br/>(3629, kegg, BioSystems)","retinol biosynthesis<br/>(1744, biocyc, BioSystems)","retinol biosynthesis<br/>(1780, humancyc, PC)","RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways<br/>(3331, reactome, PC)","RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways<br/>(3347, reactome, BioSystems)","Unfolded Protein Response (UPR)<br/>(3319, reactome, PC)","Unfolded Protein Response (UPR)<br/>(3430, reactome, BioSystems)","SREBF and miR33 in cholesterol and lipid homeostasis<br/>(1677, wiki, BioSystems)"],[30,30,50,58,4,11,17,10,10,15,17,7,8,4,8,6,10,23,19,10,7,121,11,123,359,130,132,40,134,41,136,257,2,13,67,41,24,9,56,13,6,121,123,25,8,209,39,40,214,85,13,28,7,69,133,71,28,30,33,31,137,28,30,29,28,32,30,29,31,29,31,33,31,31,32,31,96,34,32,32,32,33,34,32,35,35,5,33,36,40,120,41,117,17,18,77,78,75,85,16],[2314,2625,3969,4473,266,768,1121,633,647,1467,1140,245,312,268,331,512,428,1928,1509,915,563,7862,1050,7951,25071,8329,8418,4181,8586,4241,8675,16977,242,1276,6165,2638,2017,1009,5577,1229,569,8713,8805,2046,906,15078,4555,4555,15341,6873,1453,2241,708,5265,9784,5413,2151,2231,2399,2318,10042,2120,2120,2238,2120,2329,2258,2207,2207,2207,2286,2443,2326,2345,2338,2313,8648,2530,2373,2413,2400,2425,2492,2528,2544,2579,506,2615,2631,2922,8747,3009,9123,1332,1349,4944,4963,5991,6606,1425],[113.926243202026,113.331825297225,95.5213699618521,89.8248311366294,81.0801952850626,79.8128560504969,79.1737584116098,75.590329933673,75.3206999126494,68.4772956266237,59.7330298984967,45.9983521775178,45.2513496050825,41.7197015828896,41.6020091923876,41.385201552958,40.4472427126563,32.3009863437986,27.4385472000009,25.5388849967818,25.2336637991113,24.4972314059456,24.3996250583062,24.3814217309385,24.1367322122408,24.1342842553861,24.0249518795433,23.9189177531851,23.8743374756989,23.8102380067502,23.7483584121553,23.5074887424623,23.3443490243845,22.3106074444477,21.6217224505268,21.3035434100573,20.6023442426548,19.7231722125,19.6801676489894,19.3478466124119,19.0674310118394,18.5374921131794,18.4377364152177,18.2581873305786,18.0552382876295,18.0306114555775,17.8911799804717,17.8911799804717,17.8557780952709,17.6184974362369,17.4264167791213,17.3555333990359,17.2390893963588,17.2056719052467,17.1013950728951,17.0900564047093,17.0429817605736,16.9966087626437,16.8774137501788,16.8555260067335,16.8534314314484,16.8186075309059,16.8186075309059,16.8156358215206,16.8079207641934,16.7792574900288,16.7134983493147,16.6836143577145,16.6836143577145,16.6757228941115,16.5727608406042,16.5648749615677,16.5321791932153,16.4970931575988,16.4544312652584,16.4377566559186,16.4113466982663,16.3825572565677,16.3823755247856,16.3448802259438,16.2540494597348,16.2508532303764,16.1624044211698,16.1148775795585,16.0381533466559,15.9770665121165,15.9382488291198,15.9258469113185,15.8701972908967,15.6804153234579,15.6644406056259,15.5305664754163,14.6598000944299,14.0978147202276,13.9766299697834,12.6808232412818,12.6466619449859,12.5888877488284,11.7414433805024,11.2845790639399],["-3.8078<br/>[-3.8117, -3.7695]","-3.8092<br/>[-3.8132, -3.7709]","-3.8090<br/>[-3.8129, -3.7706]","-3.8091<br/>[-3.8131, -3.7708]","-3.7102<br/>[-3.7134, -3.6795]","-3.7101<br/>[-3.7133, -3.6793]","-3.7102<br/>[-3.7134, -3.6794]","-3.7103<br/>[-3.7134, -3.6795]","-3.7101<br/>[-3.7133, -3.6793]","-3.7658<br/>[-3.7693, -3.7314]","-3.7557<br/>[-3.7592, -3.7212]","-3.7123<br/>[-3.7155, -3.6814]","-3.7123<br/>[-3.7155, -3.6814]","-3.7126<br/>[-3.7158, -3.6817]","-3.7123<br/>[-3.7155, -3.6814]","-3.7403<br/>[-3.7437, -3.7077]","-3.7123<br/>[-3.7155, -3.6814]","-3.7383<br/>[-3.7417, -3.7050]","-3.7367<br/>[-3.7400, -3.7043]","-3.7357<br/>[-3.7391, -3.7026]","-3.7351<br/>[-3.7384, -3.7026]","-3.7250<br/>[-3.7282, -3.6934]","-3.7357<br/>[-3.7391, -3.7026]","-3.7250<br/>[-3.7282, -3.6933]","-3.7321<br/>[-3.7354, -3.7001]","-3.7250<br/>[-3.7282, -3.6934]","-3.7250<br/>[-3.7282, -3.6933]","-3.7284<br/>[-3.7317, -3.6967]","-3.7249<br/>[-3.7282, -3.6933]","-3.7284<br/>[-3.7317, -3.6967]","-3.7249<br/>[-3.7281, -3.6933]","-3.7284<br/>[-3.7316, -3.6966]","-3.7247<br/>[-3.7280, -3.6923]","-3.7357<br/>[-3.7391, -3.7025]","-3.7443<br/>[-3.7477, -3.7113]","-3.7366<br/>[-3.7399, -3.7041]","-3.7320<br/>[-3.7353, -3.6999]","-3.7214<br/>[-3.7247, -3.6899]","-3.7491<br/>[-3.7526, -3.7151]","-3.7329<br/>[-3.7362, -3.7006]","-3.7242<br/>[-3.7275, -3.6926]","-3.7189<br/>[-3.7222, -3.6877]","-3.7189<br/>[-3.7221, -3.6877]","-3.7325<br/>[-3.7358, -3.7003]","-3.7213<br/>[-3.7245, -3.6898]","-3.7219<br/>[-3.7251, -3.6904]","-3.7366<br/>[-3.7399, -3.7042]","-3.7366<br/>[-3.7399, -3.7042]","-3.7218<br/>[-3.7250, -3.6904]","-3.7414<br/>[-3.7447, -3.7088]","-3.7209<br/>[-3.7241, -3.6894]","-3.7325<br/>[-3.7358, -3.7002]","-3.7272<br/>[-3.7307, -3.6938]","-3.7188<br/>[-3.7220, -3.6875]","-3.7219<br/>[-3.7252, -3.6904]","-3.7188<br/>[-3.7220, -3.6875]","-3.7150<br/>[-3.7182, -3.6840]","-3.7150<br/>[-3.7182, -3.6840]","-3.7363<br/>[-3.7397, -3.7031]","-3.7150<br/>[-3.7182, -3.6840]","-3.7219<br/>[-3.7251, -3.6903]","-3.7149<br/>[-3.7181, -3.6838]","-3.7149<br/>[-3.7181, -3.6838]","-3.7150<br/>[-3.7181, -3.6839]","-3.7149<br/>[-3.7181, -3.6838]","-3.7374<br/>[-3.7407, -3.7048]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7149<br/>[-3.7181, -3.6839]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7345<br/>[-3.7378, -3.7022]","-3.7149<br/>[-3.7181, -3.6839]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7180, -3.6838]","-3.7148<br/>[-3.7179, -3.6837]","-3.7147<br/>[-3.7179, -3.6837]","-3.7215<br/>[-3.7248, -3.6900]","-3.7148<br/>[-3.7179, -3.6837]","-3.7147<br/>[-3.7179, -3.6837]","-3.7148<br/>[-3.7179, -3.6837]","-3.7177<br/>[-3.7209, -3.6865]","-3.7147<br/>[-3.7179, -3.6837]","-3.7130<br/>[-3.7162, -3.6821]","-3.7246<br/>[-3.7279, -3.6923]","-3.7246<br/>[-3.7279, -3.6923]","-3.7377<br/>[-3.7410, -3.7052]","-3.7377<br/>[-3.7410, -3.7052]","-3.7321<br/>[-3.7354, -3.7000]","-3.7319<br/>[-3.7353, -3.6998]","-3.7253<br/>[-3.7285, -3.6937]"],["-1.3258<br/>[-1.3444, -1.2359]","-1.3605<br/>[-1.3688, -1.3464]","-1.5122<br/>[-1.5355, -1.4855]","-1.5419<br/>[-1.6011, -1.5145]","-1.8793<br/>[-1.9364, -1.8198]","-2.3290<br/>[-2.3965, -2.2633]","-2.3895<br/>[-2.4294, -2.3274]","-2.3560<br/>[-2.4706, -2.2542]","-2.4488<br/>[-2.5018, -2.3813]","-1.3076<br/>[-1.3222, -1.2914]","-1.3250<br/>[-1.3789, -1.2998]","-1.6150<br/>[-1.6374, -1.5784]","-1.7034<br/>[-1.7232, -1.6680]","-1.7607<br/>[-1.8125, -1.7001]","-1.7640<br/>[-1.9863, -1.7298]","-1.0907<br/>[-1.0959, -1.0749]","-2.0062<br/>[-2.0355, -1.9567]","-1.7459<br/>[-1.7473, -1.7456]","-1.6802<br/>[-1.7563, -1.6242]","-1.4589<br/>[-1.5063, -1.4215]","-1.3911<br/>[-1.4021, -1.3885]","-2.4035<br/>[-2.4390, -2.3448]","-1.5154<br/>[-1.5531, -1.4770]","-2.4092<br/>[-2.4431, -2.3483]","-2.6668<br/>[-2.7023, -2.6155]","-2.4249<br/>[-2.4546, -2.3422]","-2.4302<br/>[-2.5052, -2.3689]","-2.2149<br/>[-2.2807, -2.1606]","-2.4373<br/>[-2.5209, -2.3790]","-2.2217<br/>[-2.2882, -2.1684]","-2.4438<br/>[-2.5245, -2.3822]","-2.5972<br/>[-2.6522, -2.5575]","-1.0795<br/>[-1.1375, -1.0209]","-1.6042<br/>[-1.6480, -1.5606]","-2.1598<br/>[-2.1710, -2.1380]","-1.9499<br/>[-1.9804, -1.9340]","-1.9153<br/>[-1.9524, -1.8983]","-2.0128<br/>[-2.0604, -1.9288]","-2.0975<br/>[-2.1152, -2.0710]","-1.7169<br/>[-1.7346, -1.7056]","-1.5925<br/>[-1.6188, -1.5269]","-2.5045<br/>[-2.6291, -2.4390]","-2.5106<br/>[-2.6329, -2.4422]","-1.8631<br/>[-1.9079, -1.8366]","-2.0384<br/>[-2.0972, -1.8672]","-2.6872<br/>[-2.7653, -2.5895]","-2.0290<br/>[-2.0299, -2.0290]","-2.0290<br/>[-2.0299, -2.0290]","-2.7005<br/>[-2.7716, -2.5994]","-2.2653<br/>[-2.3083, -2.2210]","-1.9684<br/>[-2.2490, -1.9267]","-1.9002<br/>[-1.9315, -1.8628]","-1.5231<br/>[-1.5918, -1.4445]","-2.4013<br/>[-2.5017, -2.3364]","-2.5702<br/>[-2.6869, -2.4987]","-2.4097<br/>[-2.5177, -2.3454]","-2.1107<br/>[-2.1742, -2.0269]","-2.1147<br/>[-2.1873, -2.0234]","-1.7448<br/>[-1.7577, -1.7342]","-2.1337<br/>[-2.1960, -2.0429]","-2.5883<br/>[-2.6966, -2.5112]","-2.1166<br/>[-2.1802, -2.0309]","-2.1166<br/>[-2.1802, -2.0309]","-2.1330<br/>[-2.1913, -2.0466]","-2.1177<br/>[-2.1802, -2.0323]","-1.9408<br/>[-1.9706, -1.9361]","-2.1394<br/>[-2.1969, -2.0535]","-2.1377<br/>[-2.1938, -2.0544]","-2.1377<br/>[-2.1938, -2.0544]","-2.1388<br/>[-2.1941, -2.0557]","-2.1515<br/>[-2.2046, -2.0834]","-2.1629<br/>[-2.2165, -2.0907]","-2.1560<br/>[-2.2162, -2.0888]","-2.1592<br/>[-2.2113, -2.0909]","-2.1631<br/>[-2.2134, -2.0948]","-2.1612<br/>[-2.2112, -2.0936]","-2.4700<br/>[-2.5472, -2.4121]","-2.1806<br/>[-2.2297, -2.1054]","-2.1698<br/>[-2.2168, -2.0991]","-2.1743<br/>[-2.2205, -2.1006]","-2.1794<br/>[-2.2233, -2.1051]","-2.1814<br/>[-2.2252, -2.1062]","-2.1915<br/>[-2.2343, -2.1169]","-2.1983<br/>[-2.2412, -2.1218]","-2.2025<br/>[-2.2442, -2.1236]","-2.2087<br/>[-2.2492, -2.1275]","-1.2116<br/>[-1.2583, -1.1959]","-2.2146<br/>[-2.2539, -2.1359]","-2.2178<br/>[-2.2568, -2.1377]","-2.2418<br/>[-2.2974, -2.1668]","-2.5903<br/>[-2.7027, -2.5054]","-2.2515<br/>[-2.2900, -2.1660]","-2.7576<br/>[-2.7773, -2.7379]","-1.7671<br/>[-1.8390, -1.7062]","-1.7721<br/>[-1.8261, -1.7102]","-2.2637<br/>[-2.3348, -2.1364]","-2.2660<br/>[-2.3362, -2.1376]","-2.3323<br/>[-2.4064, -2.2636]","-2.3843<br/>[-2.4602, -2.3217]","-1.8729<br/>[-1.9459, -1.8149]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Pathway name<br/>(ID, database, repository)<\/th>\n <th># of genes<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2,3]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 3, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-highly-expressed-genes" class="section level3">
<h3>Tissue highly expressed genes</h3>
<div id="htmlwidget-0aaad034f4771159c3b9" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-0aaad034f4771159c3b9">{"x":{"filter":"none","data":[["Liver","Muscle - Skeletal","Adrenal Gland","Testis","Brain - Anterior cingulate cortex (BA24)","Brain - Cortex","Heart - Atrial Appendage","Brain - Hypothalamus","Brain - Frontal Cortex (BA9)","Brain - Putamen (basal ganglia)","Brain - Cerebellum","Small Intestine - Terminal Ileum","Artery - Tibial","Artery - Coronary","Brain - Nucleus accumbens (basal ganglia)","Adipose - Visceral (Omentum)","Esophagus - Gastroesophageal Junction","Skin - Sun Exposed (Lower leg)","Lung","Heart - Left Ventricle","Whole Blood","Breast - Mammary Tissue","Nerve - Tibial","Uterus","Colon - Transverse","Stomach","Skin - Not Sun Exposed (Suprapubic)","Brain - Cerebellar Hemisphere","Brain - Caudate (basal ganglia)","Pancreas","Spleen","Cells - EBV-transformed lymphocytes","Brain - Hippocampus","Esophagus - Mucosa","Colon - Sigmoid","Esophagus - Muscularis","Artery - Aorta","Prostate","Adipose - Subcutaneous","Vagina","Thyroid","Cells - Transformed fibroblasts","Ovary","Pituitary"],[6049,5351,5361,5554,5641,5558,5552,5641,5928,6274,5397,4477,5774,5895,5840,5565,5533,5430,4780,5343,5605,5307,5424,5411,4968,5012,5491,5376,6208,4876,3839,4742,5488,5352,5630,5725,6065,5325,5368,5508,5886,5844,5596,5617],[20.1779482479589,17.5156452012625,13.0640145885854,12.2270034263219,11.5226316579479,11.3583262930424,10.6946279377768,10.618990653961,10.2707556459392,10.2071534517045,9.73602040518488,9.73499877825709,9.69760201729083,9.65379329164745,8.71268643009798,8.65033864046293,8.32346337642094,8.0151290982851,7.90194815170935,7.42118705954695,7.35016213973658,7.30862805939315,7.24604275614003,6.71617919248609,6.63034087144231,6.57395568837911,6.14961736259321,6.03667110906785,5.84853882796849,5.70788148620553,5.32295828445346,5.23310251270908,5.14174719665212,4.81543856547326,3.96354205746793,3.92309347532381,3.21312673587092,1.82638136438621,1.59877462087125,1.42627506335266,1.32238552571937,0.85801524288701,0.172518971395434,0.0426198712799943],["-3.7190<br/>[-3.7222, -3.6877]","-3.7210<br/>[-3.7242, -3.6897]","-3.7230<br/>[-3.7262, -3.6914]","-3.7176<br/>[-3.7208, -3.6865]","-3.7204<br/>[-3.7236, -3.6890]","-3.7202<br/>[-3.7234, -3.6888]","-3.7222<br/>[-3.7254, -3.6908]","-3.7203<br/>[-3.7236, -3.6890]","-3.7201<br/>[-3.7233, -3.6887]","-3.7223<br/>[-3.7255, -3.6908]","-3.7184<br/>[-3.7216, -3.6872]","-3.7143<br/>[-3.7175, -3.6833]","-3.7155<br/>[-3.7187, -3.6846]","-3.7155<br/>[-3.7187, -3.6845]","-3.7225<br/>[-3.7258, -3.6910]","-3.7145<br/>[-3.7177, -3.6836]","-3.7162<br/>[-3.7194, -3.6851]","-3.7117<br/>[-3.7151, -3.6793]","-3.7154<br/>[-3.7186, -3.6845]","-3.7171<br/>[-3.7203, -3.6860]","-3.7179<br/>[-3.7212, -3.6867]","-3.7146<br/>[-3.7177, -3.6837]","-3.7145<br/>[-3.7177, -3.6836]","-3.7104<br/>[-3.7135, -3.6798]","-3.7100<br/>[-3.7131, -3.6793]","-3.7100<br/>[-3.7131, -3.6793]","-3.7158<br/>[-3.7193, -3.6831]","-3.7139<br/>[-3.7171, -3.6829]","-3.7225<br/>[-3.7257, -3.6909]","-3.7098<br/>[-3.7130, -3.6792]","-3.7099<br/>[-3.7130, -3.6792]","-3.7100<br/>[-3.7131, -3.6793]","-3.7180<br/>[-3.7213, -3.6868]","-3.7112<br/>[-3.7146, -3.6787]","-3.7162<br/>[-3.7194, -3.6851]","-3.7162<br/>[-3.7194, -3.6851]","-3.7144<br/>[-3.7176, -3.6835]","-3.7099<br/>[-3.7131, -3.6793]","-3.7145<br/>[-3.7176, -3.6835]","-3.7144<br/>[-3.7176, -3.6835]","-3.7143<br/>[-3.7175, -3.6834]","-3.7100<br/>[-3.7132, -3.6794]","-3.7100<br/>[-3.7131, -3.6794]","-3.7097<br/>[-3.7128, -3.6790]"],["-2.3651<br/>[-2.3872, -2.3253]","-2.4414<br/>[-2.4691, -2.3939]","-2.2923<br/>[-2.3029, -2.2629]","-2.5529<br/>[-2.6112, -2.4875]","-2.5104<br/>[-2.5526, -2.4514]","-2.5079<br/>[-2.5457, -2.4480]","-2.6563<br/>[-2.7321, -2.5696]","-2.6022<br/>[-2.7036, -2.5094]","-2.6352<br/>[-2.7409, -2.5393]","-2.6518<br/>[-2.7638, -2.5552]","-2.5561<br/>[-2.5991, -2.4831]","-2.4787<br/>[-2.5156, -2.4038]","-2.5880<br/>[-2.6909, -2.5037]","-2.5938<br/>[-2.6942, -2.5060]","-2.6195<br/>[-2.7231, -2.5274]","-2.3854<br/>[-2.5510, -2.3394]","-2.6938<br/>[-2.7669, -2.6121]","-2.6493<br/>[-2.7338, -2.5599]","-2.6534<br/>[-2.7823, -2.5480]","-2.7347<br/>[-2.8562, -2.6317]","-2.6393<br/>[-2.7384, -2.5541]","-2.7256<br/>[-2.8724, -2.6103]","-2.7345<br/>[-2.8820, -2.6118]","-2.7923<br/>[-2.9412, -2.6727]","-2.7906<br/>[-2.9447, -2.6721]","-2.8025<br/>[-2.9531, -2.6845]","-2.8197<br/>[-2.9469, -2.7160]","-2.9160<br/>[-3.0571, -2.8102]","-2.5875<br/>[-2.6857, -2.4985]","-2.9411<br/>[-3.1123, -2.8073]","-3.0098<br/>[-3.1724, -2.8599]","-3.0626<br/>[-3.2326, -2.9076]","-2.5315<br/>[-2.6353, -2.4454]","-3.0592<br/>[-3.1962, -2.9396]","-2.6274<br/>[-2.7119, -2.5830]","-2.6325<br/>[-2.7199, -2.5834]","-2.6687<br/>[-2.7718, -2.5793]","-2.7344<br/>[-2.8716, -2.6245]","-2.7642<br/>[-2.9029, -2.6489]","-2.7988<br/>[-2.9222, -2.6883]","-2.8218<br/>[-2.9568, -2.7116]","-2.8601<br/>[-3.0414, -2.7329]","-2.9816<br/>[-3.1729, -2.8660]","-3.0142<br/>[-3.1934, -2.8706]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Tissue name<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-selectively-expressed-genes" class="section level3">
<h3>Tissue selectively expressed genes</h3>
<div id="htmlwidget-9dd0ac780160f191cf9f" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-9dd0ac780160f191cf9f">{"x":{"filter":"none","data":[["Kidney_Cortex","Uterus","Adipose_Visceral_(Omentum)","Liver","Adipose_Subcutaneous","Adrenal_Gland","Breast_Mammary_Tissue","Whole_Blood","Stomach","Heart_Atrial_Appendage","Brain_Caudate_(basal_ganglia)","Spleen","Lung","Thyroid","Nerve_Tibial","Small_Intestine_Terminal_Ileum","Muscle_Skeletal","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Nucleus_accumbens_(basal_ganglia)","Esophagus_Muscularis","Brain_Putamen_(basal_ganglia)","Artery_Tibial","Heart_Left_Ventricle","Artery_Aorta","Esophagus_Gastroesophageal_Junction","Skin_Sun_Exposed_(Lower_leg)","Skin_Not_Sun_Exposed_(Suprapubic)","Artery_Coronary","Colon_Sigmoid","Pancreas","Testis","Cells_EBV-transformed_lymphocytes","Colon_Transverse","Ovary","Prostate","Brain_Cortex","Vagina","Brain_Substantia_nigra","Cells_Transformed_fibroblasts","Pituitary","Brain_Hypothalamus","Brain_Spinal_cord_(cervical_c-1)","Brain_Hippocampus","Minor_Salivary_Gland","Esophagus_Mucosa","Brain_Frontal_Cortex_(BA9)","Brain_Amygdala","Brain_Cerebellum","Brain_Cerebellar_Hemisphere"],[8546,12030,9405,7802,9709,11764,9406,6787,8856,10636,11221,6835,7959,11537,11965,8318,8255,12484,10900,13749,11293,12095,10541,13755,13579,6478,6561,11905,10522,7325,7350,7444,7141,11108,8708,11475,6416,12225,10340,9111,11716,12196,10490,8002,6519,13166,10757,10458,13068],[8.56159569154895,7.89804215047615,7.23323432897412,5.80917061821526,4.69685447572984,4.31604242244703,2.57713820315907,1.26300106748878,1.07159867536375,0.995181269338993,0.838788033209964,0.661348376393602,0.58432156391616,0.377699496841707,0.164939886425024,0.104107487073083,-0.233176519268453,-0.349384045903328,-0.493728462206134,-0.59933004979628,-0.615743476155149,-0.727771100720054,-0.753032816217442,-0.762473007312877,-0.800992485436152,-0.813015404797777,-0.815233835500331,-0.82693399432574,-0.841998038312565,-0.845356363831092,-0.916634123155574,-0.938087377293796,-0.969171729303845,-1.02013346202496,-1.04656598737408,-1.09931825679542,-1.11563095412984,-1.12186284035495,-1.13853388973771,-1.16696044155289,-1.17878204368592,-1.32211310674289,-1.34025745882639,-1.38788302504689,-1.49434923865068,-1.63850046579848,-2.89538814057726,-3.20827884508297,-3.37259245455917],["-3.7343<br/>[-3.7376, -3.7020]","-3.7268<br/>[-3.7301, -3.6943]","-3.7301<br/>[-3.7334, -3.6982]","-3.7296<br/>[-3.7329, -3.6978]","-3.7264<br/>[-3.7297, -3.6948]","-3.7187<br/>[-3.7219, -3.6873]","-3.7248<br/>[-3.7281, -3.6931]","-3.7135<br/>[-3.7167, -3.6827]","-3.7151<br/>[-3.7183, -3.6841]","-3.7136<br/>[-3.7168, -3.6828]","-3.7135<br/>[-3.7167, -3.6826]","-3.7114<br/>[-3.7145, -3.6806]","-3.7129<br/>[-3.7161, -3.6821]","-3.7184<br/>[-3.7216, -3.6870]","-3.7185<br/>[-3.7217, -3.6871]","-3.7134<br/>[-3.7166, -3.6825]","-3.7133<br/>[-3.7165, -3.6825]","-3.7130<br/>[-3.7162, -3.6821]","-3.7114<br/>[-3.7146, -3.6806]","-3.7112<br/>[-3.7146, -3.6787]","-3.7134<br/>[-3.7166, -3.6825]","-3.7076<br/>[-3.7107, -3.6769]","-3.7115<br/>[-3.7147, -3.6808]","-3.7077<br/>[-3.7108, -3.6770]","-3.7096<br/>[-3.7127, -3.6789]","-3.7093<br/>[-3.7125, -3.6786]","-3.7093<br/>[-3.7125, -3.6787]","-3.7085<br/>[-3.7117, -3.6779]","-3.7081<br/>[-3.7112, -3.6775]","-3.7093<br/>[-3.7124, -3.6786]","-3.7099<br/>[-3.7130, -3.6792]","-3.7087<br/>[-3.7119, -3.6781]","-3.7100<br/>[-3.7132, -3.6793]","-3.7097<br/>[-3.7128, -3.6789]","-3.7109<br/>[-3.7141, -3.6801]","-3.7131<br/>[-3.7163, -3.6822]","-3.7086<br/>[-3.7118, -3.6779]","-3.7094<br/>[-3.7126, -3.6786]","-3.7096<br/>[-3.7128, -3.6788]","-3.7085<br/>[-3.7116, -3.6779]","-3.7109<br/>[-3.7141, -3.6802]","-3.7071<br/>[-3.7103, -3.6765]","-3.7134<br/>[-3.7166, -3.6824]","-3.7105<br/>[-3.7137, -3.6797]","-3.7103<br/>[-3.7137, -3.6779]","-3.7126<br/>[-3.7158, -3.6816]","-3.7131<br/>[-3.7163, -3.6822]","-3.7100<br/>[-3.7131, -3.6792]","-3.7090<br/>[-3.7122, -3.6783]"],["-2.5532<br/>[-2.6316, -2.4866]","-2.7964<br/>[-2.8130, -2.7962]","-2.4955<br/>[-2.6603, -2.3812]","-2.5544<br/>[-2.6425, -2.4762]","-2.6572<br/>[-2.7468, -2.5924]","-2.8264<br/>[-2.8284, -2.8246]","-2.8192<br/>[-2.9193, -2.7285]","-3.0307<br/>[-3.1170, -2.8701]","-3.2214<br/>[-3.3474, -3.0946]","-3.2192<br/>[-3.3512, -3.0933]","-3.1092<br/>[-3.1681, -3.0043]","-3.3188<br/>[-3.4092, -3.2275]","-3.3764<br/>[-3.4810, -3.2391]","-3.1044<br/>[-3.2106, -2.9918]","-3.1206<br/>[-3.2357, -3.0257]","-3.0696<br/>[-3.2057, -2.9501]","-3.1431<br/>[-3.3015, -3.0078]","-3.1430<br/>[-3.2728, -3.0392]","-3.1484<br/>[-3.2936, -3.0317]","-3.3104<br/>[-3.4056, -3.2021]","-3.2835<br/>[-3.3890, -3.1484]","-3.3528<br/>[-3.4477, -3.2411]","-3.2891<br/>[-3.4510, -3.1692]","-3.3659<br/>[-3.4673, -3.2478]","-3.3839<br/>[-3.4794, -3.2645]","-3.4065<br/>[-3.5564, -3.2286]","-3.4071<br/>[-3.5575, -3.2329]","-3.3940<br/>[-3.5035, -3.2659]","-3.4076<br/>[-3.5106, -3.2782]","-3.4225<br/>[-3.5620, -3.2453]","-3.4831<br/>[-3.6523, -3.2824]","-3.5166<br/>[-3.6317, -3.3538]","-3.5416<br/>[-3.7338, -3.3147]","-3.5347<br/>[-3.6400, -3.3959]","-3.3053<br/>[-3.4446, -3.1590]","-3.1256<br/>[-3.2391, -3.0279]","-3.9162<br/>[-4.1064, -3.6768]","-3.6727<br/>[-3.7692, -3.5338]","-3.6946<br/>[-3.7760, -3.5685]","-3.7930<br/>[-3.9542, -3.5800]","-3.3807<br/>[-3.4920, -3.2512]","-4.0019<br/>[-4.1284, -3.8221]","-3.1407<br/>[-3.2692, -3.0239]","-3.5771<br/>[-3.6957, -3.4174]","-3.5939<br/>[-3.7161, -3.4393]","-3.2705<br/>[-3.3686, -3.1693]","-3.1817<br/>[-3.3054, -3.0739]","-3.4647<br/>[-3.5494, -3.3445]","-3.5711<br/>[-3.6385, -3.4688]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Tissue name<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="cluster-distinctively-expressed-genes" class="section level3">
<h3>Cluster distinctively expressed genes</h3>
<div id="htmlwidget-798b325e8770e69abc2e" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-798b325e8770e69abc2e">{"x":{"filter":"none","data":[["20","18","3","10","13","17","9","19","5","1","14","12","11","4","7","6","8","16","15","2"],[7644,6884,9554,7849,7157,7959,9065,5553,10928,7016,8925,6819,9848,11776,7751,8324,9692,9733,7280,8429],[16.3864366966289,13.8129312275316,8.584444880067,4.96540025840368,4.15156973684737,3.11624469561057,2.99735492739141,0.551892954845,0.382508500862703,0.207606430771853,-0.193964619232023,-0.379730404216116,-0.453960007085027,-0.495797540216702,-0.52285707755788,-0.711704569927584,-0.714602034408835,-0.931500888784892,-1.30294708325036,-2.23240505596636],["-3.7193<br/>[-3.7225, -3.6881]","-3.7322<br/>[-3.7356, -3.7001]","-3.7288<br/>[-3.7320, -3.6969]","-3.7223<br/>[-3.7256, -3.6908]","-3.7232<br/>[-3.7265, -3.6917]","-3.7187<br/>[-3.7221, -3.6858]","-3.7211<br/>[-3.7243, -3.6896]","-3.7094<br/>[-3.7125, -3.6787]","-3.7121<br/>[-3.7152, -3.6813]","-3.7105<br/>[-3.7137, -3.6798]","-3.7131<br/>[-3.7163, -3.6822]","-3.7090<br/>[-3.7122, -3.6784]","-3.7094<br/>[-3.7125, -3.6787]","-3.7127<br/>[-3.7159, -3.6820]","-3.7126<br/>[-3.7158, -3.6818]","-3.7108<br/>[-3.7142, -3.6784]","-3.7119<br/>[-3.7151, -3.6811]","-3.7153<br/>[-3.7185, -3.6843]","-3.7105<br/>[-3.7138, -3.6780]","-3.7131<br/>[-3.7162, -3.6821]"],["-2.3777<br/>[-2.4013, -2.3408]","-2.3611<br/>[-2.4319, -2.2835]","-2.3676<br/>[-2.3720, -2.3418]","-2.7418<br/>[-2.8585, -2.6386]","-2.6143<br/>[-2.7321, -2.5986]","-2.7712<br/>[-2.8952, -2.6706]","-2.9118<br/>[-2.9661, -2.8311]","-2.9014<br/>[-3.1647, -2.7534]","-3.0818<br/>[-3.2426, -2.9852]","-3.0541<br/>[-3.2015, -2.9498]","-3.1954<br/>[-3.3344, -3.0599]","-3.2475<br/>[-3.3794, -3.1004]","-3.2821<br/>[-3.4498, -3.1123]","-3.3165<br/>[-3.4582, -3.1738]","-3.3200<br/>[-3.4670, -3.1550]","-3.4467<br/>[-3.5871, -3.2725]","-3.4437<br/>[-3.5589, -3.2986]","-2.9166<br/>[-3.1276, -2.8233]","-3.5378<br/>[-3.6809, -3.3643]","-3.1512<br/>[-3.3541, -2.9599]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Cluster ID<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
<p>The relationship between tissues and clusters is shown in Figure 1 of <a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006599">Dey et al. (2017)</a>; see below.</p>
<p><img src="http://journals.plos.org/plosgenetics/article/figure/image?size=large&id=10.1371/journal.pgen.1006599.g001" /></p>
</div>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">devtools<span class="op">::</span><span class="kw">session_info</span>()</a></code></pre></div>
<pre><code>Session info -------------------------------------------------------------</code></pre>
<pre><code> setting value
version R version 3.5.1 (2018-07-02)
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2018-10-05 </code></pre>
<pre><code>Packages -----------------------------------------------------------------</code></pre>
<pre><code> package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
base * 3.5.1 2018-07-05 local
bindr 0.1.1 2018-03-13 CRAN (R 3.5.0)
bindrcpp 0.2.2 2018-03-29 CRAN (R 3.5.0)
compiler 3.5.1 2018-07-05 local
crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
crosstalk 1.0.0 2016-12-21 CRAN (R 3.5.0)
datasets * 3.5.1 2018-07-05 local
devtools 1.13.6 2018-06-27 CRAN (R 3.5.0)
digest 0.6.17 2018-09-12 CRAN (R 3.5.0)
dplyr * 0.7.6 2018-06-29 CRAN (R 3.5.1)
DT * 0.4 2018-01-30 CRAN (R 3.5.0)
evaluate 0.11 2018-07-17 CRAN (R 3.5.0)
git2r 0.23.0 2018-07-17 CRAN (R 3.5.0)
glue 1.3.0 2018-07-17 CRAN (R 3.5.0)
graphics * 3.5.1 2018-07-05 local
grDevices * 3.5.1 2018-07-05 local
htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
htmlwidgets 1.3 2018-09-30 CRAN (R 3.5.0)
httpuv 1.4.5 2018-07-19 CRAN (R 3.5.0)
jsonlite 1.5 2017-06-01 CRAN (R 3.5.0)
knitr 1.20 2018-02-20 CRAN (R 3.5.0)
later 0.7.5 2018-09-18 CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods * 3.5.1 2018-07-05 local
mime 0.5 2016-07-07 CRAN (R 3.5.0)
pillar 1.3.0 2018-07-14 CRAN (R 3.5.0)
pkgconfig 2.0.2 2018-08-16 CRAN (R 3.5.0)
plyr * 1.8.4 2016-06-08 CRAN (R 3.5.0)
promises 1.0.1 2018-04-13 CRAN (R 3.5.0)
purrr 0.2.5 2018-05-29 CRAN (R 3.5.0)
R.matlab * 3.6.2 2018-09-27 CRAN (R 3.5.0)
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.5.0)
R.oo 1.22.0 2018-04-22 CRAN (R 3.5.0)
R.utils 2.7.0 2018-08-27 CRAN (R 3.5.0)
R6 2.3.0 2018-10-04 CRAN (R 3.5.0)
Rcpp 0.12.19 2018-10-01 CRAN (R 3.5.0)
rlang 0.2.2 2018-08-16 CRAN (R 3.5.0)
rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
shiny 1.1.0 2018-05-17 CRAN (R 3.5.0)
stats * 3.5.1 2018-07-05 local
stringi 1.2.4 2018-07-20 CRAN (R 3.5.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
tibble 1.4.2 2018-01-22 CRAN (R 3.5.0)
tidyselect 0.2.4 2018-02-26 CRAN (R 3.5.0)
tools 3.5.1 2018-07-05 local
utils * 3.5.1 2018-07-05 local
whisker 0.3-2 2013-04-28 CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
workflowr 1.1.1 2018-07-06 CRAN (R 3.5.0)
xtable 1.8-3 2018-08-29 CRAN (R 3.5.0)
yaml 2.2.0 2018-07-25 CRAN (R 3.5.0)</code></pre>
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