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<h1 class="title toc-ignore">Enrichment results of type 2 diabetes</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/22885922">“Large-Scale Association Analysis Provides Insights into the Genetic Architecture and Pathophysiology of Type 2 Diabetes” (<em>Nature Genetics</em>, 2012)</a>. The summary data file is available at <a href="http://diagram-consortium.org/downloads.html" class="uri">http://diagram-consortium.org/downloads.html</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>
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BioSystems)","Erythrocyte Differentiation Pathway<br/>(1584, biocarta, BioCarta)","TRAF6 mediated NF-kB activation<br/>(2071, reactome, PC)","ALKBH3 mediated reversal of alkylation damage<br/>(459, reactome, BioSystems)","Toll-Like Receptor Pathway<br/>(2442, biocarta, BioCarta)","TNF/Stress Related Signaling<br/>(2128, biocarta, BioCarta)","TRAIL signaling pathway<br/>(2122, pid, PC)","Links between Pyk2 and Map Kinases<br/>(2307, biocarta, BioCarta)","Role of MAL in Rho-Mediated Activation of SRF<br/>(1847, biocarta, BioCarta)","Osteopontin-mediated events<br/>(2431, pid, PC)","Human Cytomegalovirus and Map Kinase Pathways<br/>(1723, biocarta, BioCarta)","Osteopontin-mediated events<br/>(2508, pid, BioSystems)","JNK signaling in the CD4+ TCR pathway<br/>(1456, pid, BioSystems)","JNK signaling in the CD4+ TCR pathway<br/>(1479, pid, PC)","Regulation of cytoplasmic and nuclear SMAD2/3 signaling<br/>(1869, pid, BioSystems)","Apoptosis Modulation by HSP70<br/>(1807, wiki, BioSystems)","Ceramide Signaling Pathway<br/>(1954, biocarta, BioCarta)","Signal transduction through IL1R<br/>(2441, biocarta, BioCarta)","FAS (CD95) signaling pathway<br/>(2516, pid, PC)","Map Kinase Inactivation of SMRT Corepressor<br/>(1264, biocarta, BioCarta)","Stress Induction of HSP Regulation<br/>(1588, biocarta, BioCarta)","Regulation of cytoplasmic and nuclear SMAD2/3 signaling<br/>(1891, pid, PC)","PDGF Signaling Pathway<br/>(2440, biocarta, BioCarta)","EGF Signaling Pathway<br/>(2396, biocarta, BioCarta)","NF-kB Signaling Pathway<br/>(1905, biocarta, BioCarta)","MAPK (p38) signaling<br/>(2033, kegg, BioSystems)","IL-10 Anti-inflammatory Signaling Pathway<br/>(1724, biocarta, BioCarta)","Inhibition of Cellular Proliferation by Gleevec<br/>(2079, biocarta, BioCarta)","CD40/CD40L signaling<br/>(2356, pid, BioSystems)","MAPK (JNK) signaling<br/>(1977, kegg, BioSystems)","MAPK Cascade<br/>(2268, wiki, BioSystems)","TNF receptor signaling pathway<br/>(2787, pid, BioSystems)","FAS signaling pathway ( CD95 )<br/>(2397, biocarta, BioCarta)","TNF receptor signaling pathway <br/>(2832, pid, PC)","Rac 1 cell motility signaling pathway<br/>(2082, biocarta, BioCarta)","TNFR1 Signaling Pathway<br/>(2342, biocarta, BioCarta)","p38 MAPK Signaling Pathway<br/>(2540, wiki, BioSystems)","BCR Signaling Pathway<br/>(2485, biocarta, BioCarta)","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)","CD40/CD40L signaling<br/>(2588, pid, PC)","Fc Epsilon Receptor I Signaling in Mast Cells<br/>(2621, biocarta, BioCarta)","RIG-I-like receptor signaling pathway<br/>(3222, kegg, BioSystems)","Fc-epsilon receptor I signaling in mast cells<br/>(3074, pid, BioSystems)","RAC1 signaling pathway<br/>(3001, pid, PC)","Fc-epsilon receptor I signaling in mast cells<br/>(3105, pid, PC)","HIV-I Nef: negative effector of Fas and TNF<br/>(3070, biocarta, BioCarta)","T Cell Receptor Signaling Pathway<br/>(2802, biocarta, BioCarta)","Keratinocyte Differentiation<br/>(2869, biocarta, BioCarta)","FAS pathway and Stress induction of HSP regulation<br/>(2683, wiki, BioSystems)","Ceramide signaling pathway<br/>(2815, pid, BioSystems)","Caspase cascade in apoptosis<br/>(2954, pid, BioSystems)","p38 MAPK Signaling Pathway <br/>(2700, biocarta, BioCarta)","Cells and Molecules involved in local acute inflammatory response<br/>(1655, biocarta, BioCarta)","FCERI mediated MAPK activation<br/>(2769, reactome, PC)","T cell activation<br/>(3127, panther, PC)","fMLP induced chemokine gene expression in HMC-1 cells<br/>(2567, biocarta, BioCarta)","Ceramide signaling pathway<br/>(2882, pid, PC)","Cytokine Network<br/>(1901, biocarta, BioCarta)","Caspase Cascade in Apoptosis<br/>(3066, pid, PC)","IFN-gamma pathway<br/>(2740, pid, BioSystems)","Angiotensin II mediated activation of JNK Pathway via Pyk2 dependent signaling<br/>(2484, biocarta, BioCarta)","T cell activation<br/>(3272, panther, PANTHER)","IFN-gamma pathway<br/>(2796, pid, PC)","Interferon type I<br/>(2949, wiki, BioSystems)","Apoptosis<br/>(3382, wiki, BioSystems)","BCR signaling pathway<br/>(3172, pid, BioSystems)","Cellular roles of Anthrax toxin<br/>(1991, pid, PC)","BCR signaling pathway<br/>(3176, pid, PC)","IL27-mediated signaling events<br/>(2201, pid, PC)","TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation<br/>(3284, reactome, BioSystems)","Toll Like Receptor 5 (TLR5) Cascade<br/>(3293, reactome, BioSystems)","MyD88 dependent cascade initiated on endosome<br/>(3302, reactome, BioSystems)","Toll Like Receptor TLR6:TLR2 Cascade<br/>(3371, reactome, BioSystems)","Cytokines and Inflammatory Response<br/>(2305, biocarta, BioCarta)","Toll Like Receptor 9 (TLR9) Cascade<br/>(3336, reactome, BioSystems)","MAPKinase Signaling Pathway<br/>(3412, biocarta, BioCarta)","Role of Calcineurin-dependent NFAT signaling in lymphocytes<br/>(2994, pid, BioSystems)","TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation<br/>(3357, reactome, PC)","CDC42 signaling events<br/>(3257, pid, PC)","MyD88 cascade initiated on plasma membrane<br/>(3368, reactome, PC)","MyD88 dependent cascade initiated on endosome<br/>(3380, reactome, PC)","Role of Calcineurin-dependent NFAT signaling in lymphocytes<br/>(3038, pid, PC)","Ras Pathway<br/>(3129, panther, PANTHER)","Toll Like Receptor 9 (TLR9) Cascade<br/>(3411, reactome, PC)","Ras Pathway<br/>(3203, panther, PC)","MyD88:Mal cascade initiated on plasma membrane<br/>(3455, reactome, PC)"],[29,7,6,6,10,9,13,10,11,13,17,17,26,39,15,23,4,31,24,24,28,19,31,17,32,13,14,19,18,21,31,33,11,15,20,31,30,20,22,17,23,29,21,27,42,30,44,23,29,33,32,77,78,35,36,66,56,52,59,56,43,46,38,43,49,39,16,42,61,34,47,20,56,40,32,70,43,49,81,63,22,64,26,71,72,73,80,28,77,84,51,79,69,80,81,54,61,84,65,88],[2715,469,473,392,734,779,1208,866,1143,1008,1404,1392,2512,1394,1164,1770,459,2646,1763,1639,2816,1324,3234,1375,3315,1498,1520,1478,1667,1803,2787,2729,1635,1119,1618,2670,2792,1662,1933,1156,1837,2250,2144,2298,3424,2443,3642,2382,2253,2868,3509,5024,5044,2799,3643,3853,5302,4074,5629,4329,4234,4973,3089,3529,4039,3301,1540,4200,5861,3731,3866,1503,4852,3810,3578,6452,4081,4133,6765,5753,1948,5929,1884,6286,6364,6411,7245,1700,6792,6952,5565,6951,6942,7029,7076,5963,5798,7378,6136,7910],[442.24505364436,-0.0250694438965125,-0.0251879881592561,-0.0470313831070317,-0.0474839715265986,-0.0503176164351965,-0.0515350325543634,-0.0526111669445742,-0.0578380203022134,-0.0730250276209767,-0.0835720969962694,-0.0908745441054681,-0.113650450112338,-0.122506572962026,-0.122978577420483,-0.124523057107231,-0.133793978398278,-0.140087674730109,-0.140723334719226,-0.144907946011682,-0.167098971085829,-0.17593451602209,-0.182094501356078,-0.186114384669036,-0.188828366602947,-0.207528928654833,-0.209524908639832,-0.212978334083293,-0.215886243836833,-0.220078989544855,-0.220987458697275,-0.222491708407668,-0.224653079823414,-0.224873369240309,-0.225245471360319,-0.227798894593995,-0.236544282470585,-0.23969739279841,-0.241438552493525,-0.241792243064916,-0.243244029547242,-0.245472996384678,-0.245695690969978,-0.250411034875416,-0.254332022872889,-0.267544210257509,-0.267745017107595,-0.270522616996783,-0.272374571421231,-0.274545174105327,-0.274919260277783,-0.276592051677027,-0.277562597230226,-0.279172419855939,-0.282539790771953,-0.283936700070721,-0.285927472030164,-0.292094222746708,-0.296742756235723,-0.298019651779772,-0.3017538514287,-0.302113533224605,-0.302798445528801,-0.303990258858107,-0.306266097887205,-0.310927106655917,-0.312701071347289,-0.313665095231632,-0.313937302589471,-0.31840801298608,-0.319211639610394,-0.319266698951974,-0.319911728167357,-0.321316937674326,-0.323708871847882,-0.328959404812349,-0.333756784032384,-0.336431464194792,-0.338666560754261,-0.33947238353796,-0.341360112379935,-0.344379523004467,-0.352986119142416,-0.353444308230972,-0.357296297348741,-0.357686720004139,-0.357877990221896,-0.362007663715113,-0.369685822295053,-0.370208774763187,-0.373060115247431,-0.374948361134651,-0.376700406293714,-0.37846808766917,-0.378820354932892,-0.38271756759234,-0.383965375428738,-0.387344765721209,-0.393809238410584,-0.429940674018149],["-4.5998<br/>[-4.6696, -4.5266]","-4.6006<br/>[-4.6705, -4.5275]","-4.6006<br/>[-4.6705, -4.5275]","-4.6006<br/>[-4.6704, -4.5274]","-4.6005<br/>[-4.6703, -4.5273]","-4.6005<br/>[-4.6703, -4.5273]","-4.6008<br/>[-4.6705, -4.5278]","-4.6005<br/>[-4.6703, -4.5273]","-4.6003<br/>[-4.6701, -4.5271]","-4.6004<br/>[-4.6702, -4.5272]","-4.6008<br/>[-4.6704, -4.5277]","-4.6007<br/>[-4.6704, -4.5277]","-4.6009<br/>[-4.6704, -4.5280]","-4.6002<br/>[-4.6700, -4.5270]","-4.6003<br/>[-4.6701, -4.5271]","-4.6006<br/>[-4.6703, -4.5276]","-4.6007<br/>[-4.6705, -4.5275]","-4.6005<br/>[-4.6701, -4.5276]","-4.6006<br/>[-4.6703, -4.5276]","-4.6006<br/>[-4.6703, -4.5275]","-4.6008<br/>[-4.6704, -4.5279]","-4.6004<br/>[-4.6701, -4.5272]","-4.6007<br/>[-4.6702, -4.5278]","-4.6003<br/>[-4.6701, -4.5271]","-4.6006<br/>[-4.6701, -4.5278]","-4.6002<br/>[-4.6700, -4.5270]","-4.6002<br/>[-4.6700, -4.5270]","-4.6002<br/>[-4.6700, -4.5270]","-4.6002<br/>[-4.6700, -4.5270]","-4.6002<br/>[-4.6700, -4.5270]","-4.6002<br/>[-4.6699, -4.5272]","-4.6002<br/>[-4.6699, -4.5272]","-4.6001<br/>[-4.6700, -4.5270]","-4.6003<br/>[-4.6702, -4.5271]","-4.6001<br/>[-4.6700, -4.5269]","-4.6003<br/>[-4.6700, -4.5272]","-4.6002<br/>[-4.6699, -4.5272]","-4.6006<br/>[-4.6703, -4.5276]","-4.6001<br/>[-4.6699, -4.5269]","-4.6003<br/>[-4.6701, -4.5271]","-4.6001<br/>[-4.6699, -4.5269]","-4.6000<br/>[-4.6698, -4.5268]","-4.6000<br/>[-4.6698, -4.5268]","-4.6000<br/>[-4.6698, -4.5268]","-4.6000<br/>[-4.6697, -4.5270]","-4.5999<br/>[-4.6697, -4.5267]","-4.5999<br/>[-4.6696, -4.5270]","-4.5998<br/>[-4.6697, -4.5267]","-4.5999<br/>[-4.6697, -4.5267]","-4.5998<br/>[-4.6696, -4.5267]","-4.6000<br/>[-4.6696, -4.5270]","-4.5998<br/>[-4.6694, -4.5269]","-4.5998<br/>[-4.6694, -4.5269]","-4.5998<br/>[-4.6696, -4.5266]","-4.5999<br/>[-4.6696, -4.5269]","-4.5998<br/>[-4.6695, -4.5268]","-4.5998<br/>[-4.6693, -4.5270]","-4.6000<br/>[-4.6696, -4.5270]","-4.5997<br/>[-4.6692, -4.5269]","-4.5998<br/>[-4.6694, -4.5268]","-4.5998<br/>[-4.6694, -4.5268]","-4.5995<br/>[-4.6691, -4.5266]","-4.5996<br/>[-4.6694, -4.5265]","-4.5996<br/>[-4.6694, -4.5265]","-4.5997<br/>[-4.6694, -4.5267]","-4.5996<br/>[-4.6693, -4.5264]","-4.6002<br/>[-4.6700, -4.5271]","-4.5997<br/>[-4.6694, -4.5267]","-4.5996<br/>[-4.6691, -4.5267]","-4.5995<br/>[-4.6692, -4.5264]","-4.5995<br/>[-4.6692, -4.5264]","-4.6002<br/>[-4.6700, -4.5270]","-4.5994<br/>[-4.6691, -4.5264]","-4.5995<br/>[-4.6692, -4.5264]","-4.5995<br/>[-4.6692, -4.5263]","-4.5994<br/>[-4.6689, -4.5266]","-4.5994<br/>[-4.6691, -4.5263]","-4.5994<br/>[-4.6691, -4.5263]","-4.5988<br/>[-4.6683, -4.5258]","-4.5992<br/>[-4.6688, -4.5262]","-4.6001<br/>[-4.6699, -4.5269]","-4.5991<br/>[-4.6687, -4.5262]","-4.6000<br/>[-4.6699, -4.5268]","-4.5990<br/>[-4.6686, -4.5261]","-4.5990<br/>[-4.6686, -4.5261]","-4.5990<br/>[-4.6686, -4.5261]","-4.5989<br/>[-4.6684, -4.5261]","-4.6001<br/>[-4.6699, -4.5269]","-4.5989<br/>[-4.6684, -4.5259]","-4.5989<br/>[-4.6684, -4.5261]","-4.5988<br/>[-4.6685, -4.5257]","-4.5988<br/>[-4.6683, -4.5259]","-4.5989<br/>[-4.6685, -4.5260]","-4.5988<br/>[-4.6683, -4.5258]","-4.5988<br/>[-4.6683, -4.5258]","-4.5987<br/>[-4.6684, -4.5256]","-4.5986<br/>[-4.6684, -4.5255]","-4.5986<br/>[-4.6682, -4.5257]","-4.5985<br/>[-4.6683, -4.5254]","-4.5987<br/>[-4.6682, -4.5258]"],["-2.8744<br/>[-2.8744, -2.8710]","-3.8818<br/>[-5.0399, -3.4073]","-3.8805<br/>[-5.0389, -3.4057]","-4.5498<br/>[-5.9124, -4.0000]","-4.5862<br/>[-5.6917, -4.0871]","-4.5957<br/>[-5.7361, -4.0955]","-3.4910<br/>[-4.7338, -3.0051]","-4.4752<br/>[-5.5217, -3.9819]","-4.8853<br/>[-5.8473, -4.4086]","-4.4699<br/>[-5.6043, -3.9527]","-3.5897<br/>[-4.8301, -3.0923]","-3.6230<br/>[-4.8437, -3.1293]","-3.6748<br/>[-4.7841, -3.1741]","-4.7828<br/>[-5.9327, -4.2289]","-4.7630<br/>[-6.0117, -4.1948]","-3.7510<br/>[-4.9254, -3.2432]","-3.3712<br/>[-4.9088, -2.7880]","-3.7476<br/>[-4.9005, -3.2512]","-3.7832<br/>[-4.9400, -3.2808]","-3.8219<br/>[-4.9727, -3.3163]","-3.8451<br/>[-4.7549, -3.3387]","-4.1429<br/>[-5.3914, -3.5840]","-3.8676<br/>[-4.8186, -3.3670]","-4.2337<br/>[-5.4130, -3.6818]","-3.8863<br/>[-4.8288, -3.3864]","-4.4130<br/>[-5.6749, -3.8357]","-4.4203<br/>[-5.6410, -3.8430]","-4.5846<br/>[-5.8504, -4.0033]","-4.3735<br/>[-5.5402, -3.8293]","-4.3025<br/>[-5.4748, -3.7551]","-4.0636<br/>[-5.1074, -3.5584]","-4.0813<br/>[-5.0893, -3.5733]","-4.5725<br/>[-5.8159, -3.9968]","-4.4731<br/>[-5.8344, -3.8785]","-4.6290<br/>[-5.8692, -4.0541]","-4.1328<br/>[-5.0329, -3.6184]","-4.1622<br/>[-5.0831, -3.6512]","-3.7697<br/>[-4.9181, -3.2504]","-4.5075<br/>[-5.6791, -3.9528]","-4.6276<br/>[-5.9733, -4.0344]","-4.6994<br/>[-5.9066, -4.1304]","-4.4461<br/>[-5.5576, -3.9093]","-4.5409<br/>[-5.6869, -3.9900]","-4.4755<br/>[-5.6046, -3.9301]","-4.1408<br/>[-5.1487, -3.6379]","-4.6536<br/>[-5.7483, -4.1177]","-4.1827<br/>[-5.1725, -3.6825]","-4.8127<br/>[-5.9429, -4.2595]","-4.7848<br/>[-5.9314, -4.2286]","-4.4500<br/>[-5.4794, -3.9401]","-4.2580<br/>[-5.1146, -3.7523]","-4.1948<br/>[-5.0005, -3.7218]","-4.1975<br/>[-5.0350, -3.7255]","-4.5445<br/>[-5.6041, -4.0194]","-4.2826<br/>[-5.1620, -3.7820]","-4.2451<br/>[-5.2119, -3.7479]","-4.2032<br/>[-5.0715, -3.7224]","-4.2790<br/>[-5.0977, -3.7981]","-4.2235<br/>[-5.0500, -3.7423]","-4.2582<br/>[-5.1611, -3.7696]","-4.2989<br/>[-5.1673, -3.8065]","-4.3131<br/>[-5.2267, -3.8293]","-4.7291<br/>[-5.7317, -4.2021]","-4.4878<br/>[-5.4717, -3.9866]","-4.3694<br/>[-5.1949, -3.8767]","-4.7131<br/>[-5.7146, -4.2024]","-4.3326<br/>[-5.5902, -3.7611]","-4.3913<br/>[-5.2271, -3.9042]","-4.2845<br/>[-5.0884, -3.8082]","-4.5578<br/>[-5.5662, -4.0413]","-4.5235<br/>[-5.4888, -4.0267]","-4.5191<br/>[-5.7922, -3.9407]","-4.4625<br/>[-5.2850, -3.9847]","-4.5659<br/>[-5.5453, -4.0605]","-4.7257<br/>[-5.7492, -4.2007]","-4.3052<br/>[-5.1307, -3.8356]","-4.6045<br/>[-5.5659, -4.1026]","-4.6205<br/>[-5.5696, -4.1248]","-4.3420<br/>[-5.0265, -3.8800]","-4.4317<br/>[-5.3134, -3.9513]","-4.5019<br/>[-5.6943, -3.9402]","-4.4378<br/>[-5.2793, -3.9563]","-4.6915<br/>[-5.8934, -4.1261]","-4.4502<br/>[-5.3101, -3.9772]","-4.4652<br/>[-5.3198, -3.9942]","-4.4609<br/>[-5.3160, -3.9891]","-4.3710<br/>[-5.1930, -3.9002]","-4.6569<br/>[-5.8874, -4.0858]","-4.4887<br/>[-5.2949, -4.0192]","-4.4725<br/>[-5.3120, -4.0075]","-4.8132<br/>[-5.6909, -4.3352]","-4.5028<br/>[-5.3029, -4.0345]","-4.5323<br/>[-5.2674, -4.0930]","-4.5165<br/>[-5.3480, -4.0521]","-4.5122<br/>[-5.3442, -4.0471]","-4.7930<br/>[-5.6238, -4.3147]","-4.8786<br/>[-5.7731, -4.3889]","-4.5300<br/>[-5.3172, -4.0660]","-4.8897<br/>[-5.7708, -4.4036]","-4.4216<br/>[-5.2567, -3.9589]"]],"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":[["Whole Blood","Adrenal Gland","Brain - Hippocampus","Brain - Cerebellum","Brain - Cortex","Brain - Anterior cingulate cortex (BA24)","Brain - Hypothalamus","Brain - Nucleus accumbens (basal ganglia)","Brain - Frontal Cortex (BA9)","Brain - Putamen (basal ganglia)","Liver","Brain - Caudate (basal ganglia)","Pancreas","Spleen","Adipose - Subcutaneous","Adipose - Visceral (Omentum)","Small Intestine - Terminal Ileum","Brain - Cerebellar Hemisphere","Lung","Cells - EBV-transformed lymphocytes","Heart - Left Ventricle","Colon - Transverse","Esophagus - Mucosa","Muscle - Skeletal","Stomach","Breast - Mammary Tissue","Prostate","Skin - Sun Exposed (Lower leg)","Vagina","Skin - Not Sun Exposed (Suprapubic)","Nerve - Tibial","Uterus","Heart - Atrial Appendage","Testis","Esophagus - Gastroesophageal Junction","Pituitary","Ovary","Colon - Sigmoid","Cells - Transformed fibroblasts","Artery - Tibial","Esophagus - Muscularis","Thyroid","Artery - Coronary","Artery - Aorta"],[5688,5441,5562,5470,5631,5714,5711,5906,5993,6355,6142,6280,4948,3888,5433,5639,4551,5451,4845,4793,5421,5034,5425,5446,5080,5378,5400,5515,5596,5577,5487,5481,5645,5658,5608,5699,5675,5704,5917,5854,5799,5978,5980,6154],[56.1486478496496,33.1908236776089,-0.142267217010509,-0.147962123603254,-0.227246123699205,-0.234937254043429,-0.238860235916786,-0.246417488409496,-0.255399246096614,-0.268921047875431,-0.270254435353132,-0.272315588477082,-0.612406941037181,-0.616745553915757,-0.632738848909746,-0.639225311544257,-0.641393184593954,-0.647188703347702,-0.647352424067196,-0.65023257210928,-0.655050836471214,-0.659490900486996,-0.65979561991466,-0.65980885629403,-0.659920322294348,-0.66341435257477,-0.665006249454429,-0.665120330427703,-0.66553923737818,-0.668366160282825,-0.670789493109085,-0.672030362482853,-0.672289951024211,-0.674854473557689,-0.676208491043509,-0.677874101722278,-0.678152017111408,-0.679179728435237,-0.68058667767995,-0.682474891930292,-0.682839604650845,-0.686318807231931,-0.686447174374452,-0.691715447635932],["-4.5988<br/>[-4.6685, -4.5258]","-4.6079<br/>[-4.6767, -4.5351]","-4.6082<br/>[-4.6769, -4.5356]","-4.6082<br/>[-4.6769, -4.5355]","-4.6078<br/>[-4.6766, -4.5350]","-4.6077<br/>[-4.6766, -4.5350]","-4.6077<br/>[-4.6766, -4.5350]","-4.6077<br/>[-4.6765, -4.5349]","-4.6076<br/>[-4.6765, -4.5349]","-4.6076<br/>[-4.6764, -4.5348]","-4.6075<br/>[-4.6764, -4.5348]","-4.6075<br/>[-4.6764, -4.5348]","-4.5996<br/>[-4.6692, -4.5266]","-4.5993<br/>[-4.6691, -4.5262]","-4.5992<br/>[-4.6688, -4.5263]","-4.5992<br/>[-4.6688, -4.5262]","-4.5991<br/>[-4.6689, -4.5260]","-4.5991<br/>[-4.6687, -4.5260]","-4.5990<br/>[-4.6688, -4.5259]","-4.5990<br/>[-4.6688, -4.5259]","-4.5990<br/>[-4.6687, -4.5259]","-4.5989<br/>[-4.6687, -4.5258]","-4.5989<br/>[-4.6686, -4.5259]","-4.5989<br/>[-4.6686, -4.5259]","-4.5989<br/>[-4.6687, -4.5258]","-4.5989<br/>[-4.6686, -4.5258]","-4.5988<br/>[-4.6686, -4.5258]","-4.5989<br/>[-4.6686, -4.5258]","-4.5989<br/>[-4.6686, -4.5258]","-4.5988<br/>[-4.6685, -4.5258]","-4.5988<br/>[-4.6685, -4.5257]","-4.5988<br/>[-4.6685, -4.5257]","-4.5988<br/>[-4.6685, -4.5257]","-4.5987<br/>[-4.6685, -4.5256]","-4.5987<br/>[-4.6685, -4.5256]","-4.5987<br/>[-4.6684, -4.5256]","-4.5987<br/>[-4.6684, -4.5256]","-4.5987<br/>[-4.6684, -4.5256]","-4.5987<br/>[-4.6684, -4.5256]","-4.5986<br/>[-4.6684, -4.5255]","-4.5986<br/>[-4.6684, -4.5255]","-4.5986<br/>[-4.6683, -4.5255]","-4.5986<br/>[-4.6683, -4.5255]","-4.5985<br/>[-4.6683, -4.5254]"],["-3.0175<br/>[-3.0511, -2.9886]","-2.1548<br/>[-2.1569, -2.1468]","-3.6526<br/>[-4.0413, -3.4325]","-3.6540<br/>[-4.0326, -3.4271]","-3.7511<br/>[-4.0571, -3.5774]","-3.7608<br/>[-4.0501, -3.5845]","-3.7664<br/>[-4.0508, -3.5962]","-3.7747<br/>[-4.0827, -3.6026]","-3.7858<br/>[-4.0854, -3.6149]","-3.8014<br/>[-4.1272, -3.6257]","-3.8051<br/>[-4.0824, -3.6353]","-3.8065<br/>[-4.1241, -3.6395]","-4.3986<br/>[-5.1823, -3.9236]","-4.7679<br/>[-5.7563, -4.2442]","-4.4430<br/>[-5.3104, -3.9543]","-4.4555<br/>[-5.3156, -3.9653]","-4.8031<br/>[-5.7516, -4.2893]","-4.5501<br/>[-5.4620, -4.0518]","-4.7473<br/>[-5.6840, -4.2378]","-4.8257<br/>[-5.7226, -4.3149]","-4.6387<br/>[-5.5441, -4.1416]","-4.8615<br/>[-5.7816, -4.3553]","-4.6952<br/>[-5.5567, -4.1964]","-4.6873<br/>[-5.5886, -4.1897]","-4.8428<br/>[-5.7626, -4.3359]","-4.7608<br/>[-5.6634, -4.2612]","-4.7719<br/>[-5.6825, -4.2713]","-4.7338<br/>[-5.6270, -4.2430]","-4.7108<br/>[-5.6008, -4.2206]","-4.7560<br/>[-5.6448, -4.2640]","-4.8273<br/>[-5.7298, -4.3298]","-4.8522<br/>[-5.7536, -4.3523]","-4.7835<br/>[-5.6785, -4.2866]","-4.8171<br/>[-5.7132, -4.3199]","-4.8638<br/>[-5.7596, -4.3653]","-4.8488<br/>[-5.7429, -4.3501]","-4.8659<br/>[-5.7202, -4.3646]","-4.8700<br/>[-5.7615, -4.3696]","-4.8021<br/>[-5.6799, -4.3116]","-4.8568<br/>[-5.7426, -4.3605]","-4.8903<br/>[-5.7762, -4.3952]","-4.8673<br/>[-5.7463, -4.3749]","-4.8682<br/>[-5.7482, -4.3750]","-4.8815<br/>[-5.7167, -4.3874]"]],"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":[["Uterus","Artery_Coronary","Pancreas","Adipose_Visceral_(Omentum)","Adipose_Subcutaneous","Liver","Adrenal_Gland","Brain_Caudate_(basal_ganglia)","Colon_Transverse","Brain_Putamen_(basal_ganglia)","Esophagus_Gastroesophageal_Junction","Cells_Transformed_fibroblasts","Small_Intestine_Terminal_Ileum","Stomach","Esophagus_Muscularis","Ovary","Breast_Mammary_Tissue","Esophagus_Mucosa","Skin_Sun_Exposed_(Lower_leg)","Vagina","Skin_Not_Sun_Exposed_(Suprapubic)","Whole_Blood","Cells_EBV-transformed_lymphocytes","Thyroid","Spleen","Testis","Minor_Salivary_Gland","Lung","Muscle_Skeletal","Brain_Cerebellum","Pituitary","Kidney_Cortex","Prostate","Heart_Atrial_Appendage","Heart_Left_Ventricle","Brain_Cerebellar_Hemisphere","Colon_Sigmoid","Brain_Hippocampus","Brain_Cortex","Brain_Amygdala","Brain_Nucleus_accumbens_(basal_ganglia)","Nerve_Tibial","Brain_Hypothalamus","Brain_Spinal_cord_(cervical_c-1)","Brain_Substantia_nigra","Brain_Anterior_cingulate_cortex_(BA24)","Artery_Tibial","Brain_Frontal_Cortex_(BA9)","Artery_Aorta"],[12166,12065,7458,9565,9882,7939,11909,11383,7263,11463,13742,10536,8465,9011,13926,11271,9582,6630,6572,6544,6656,6883,7548,11664,6932,7508,8184,8070,8372,10591,9302,8693,8856,10790,10702,13204,10674,10642,11628,10915,11049,12142,11874,12374,12385,12649,12253,13324,13958],[127.82311457452,0.0759705019729847,0.00290300732569767,-0.216368286055789,-0.231850065482216,-0.375448577524957,-0.42058211806063,-0.448751622059954,-0.452943718742894,-0.454822877119517,-0.488127662362795,-0.499528689032877,-0.501577139894525,-0.508723079669492,-0.525304194484516,-0.536460780073788,-0.545587169101567,-0.697388178640413,-0.698861336262007,-0.700077984262384,-0.702299768457355,-0.706186494215982,-0.710182919836963,-0.716308669769452,-0.719305657092193,-0.722947871321608,-0.734745355697604,-0.738933431746105,-0.747255318560424,-0.750967450278494,-0.75199710830485,-0.752075369802502,-0.755963084856142,-0.788605289991873,-0.789796485119939,-0.792258178544661,-0.794022266494138,-0.79466994414008,-0.795594112800768,-0.798197593721385,-0.799898234250847,-0.814002344725684,-0.815461607976413,-0.817439608518914,-0.819235933162285,-0.820476564556624,-0.821310467043417,-0.832530050204883,-0.84651994809091],["-4.6121<br/>[-4.6837, -4.5371]","-4.6106<br/>[-4.6812, -4.5362]","-4.6158<br/>[-4.6882, -4.5404]","-4.6142<br/>[-4.6865, -4.5389]","-4.6141<br/>[-4.6864, -4.5387]","-4.6068<br/>[-4.6756, -4.5341]","-4.6070<br/>[-4.6754, -4.5346]","-4.6071<br/>[-4.6760, -4.5342]","-4.6033<br/>[-4.6720, -4.5310]","-4.6070<br/>[-4.6759, -4.5342]","-4.6067<br/>[-4.6754, -4.5341]","-4.6044<br/>[-4.6728, -4.5321]","-4.6028<br/>[-4.6715, -4.5306]","-4.6028<br/>[-4.6714, -4.5306]","-4.6062<br/>[-4.6750, -4.5334]","-4.6040<br/>[-4.6724, -4.5317]","-4.5975<br/>[-4.6671, -4.5245]","-4.5985<br/>[-4.6682, -4.5254]","-4.5984<br/>[-4.6681, -4.5254]","-4.5984<br/>[-4.6681, -4.5254]","-4.5984<br/>[-4.6681, -4.5253]","-4.5983<br/>[-4.6680, -4.5253]","-4.5984<br/>[-4.6680, -4.5254]","-4.5987<br/>[-4.6679, -4.5262]","-4.5981<br/>[-4.6679, -4.5250]","-4.5981<br/>[-4.6678, -4.5250]","-4.5979<br/>[-4.6676, -4.5249]","-4.5978<br/>[-4.6675, -4.5248]","-4.5977<br/>[-4.6674, -4.5246]","-4.5980<br/>[-4.6674, -4.5251]","-4.5974<br/>[-4.6671, -4.5244]","-4.5976<br/>[-4.6673, -4.5246]","-4.5976<br/>[-4.6672, -4.5245]","-4.5970<br/>[-4.6666, -4.5240]","-4.5969<br/>[-4.6666, -4.5240]","-4.5972<br/>[-4.6666, -4.5245]","-4.5969<br/>[-4.6665, -4.5238]","-4.5968<br/>[-4.6665, -4.5238]","-4.5968<br/>[-4.6664, -4.5239]","-4.5968<br/>[-4.6664, -4.5237]","-4.5967<br/>[-4.6664, -4.5237]","-4.5964<br/>[-4.6660, -4.5235]","-4.5964<br/>[-4.6660, -4.5234]","-4.5964<br/>[-4.6659, -4.5234]","-4.5963<br/>[-4.6659, -4.5234]","-4.5963<br/>[-4.6659, -4.5233]","-4.5963<br/>[-4.6659, -4.5233]","-4.5960<br/>[-4.6656, -4.5231]","-4.5957<br/>[-4.6653, -4.5227]"],["-3.5668<br/>[-3.5986, -3.5226]","-4.0153<br/>[-4.1064, -3.9045]","-3.6624<br/>[-3.8483, -3.4548]","-3.8592<br/>[-3.9804, -3.7062]","-3.8745<br/>[-3.9920, -3.7205]","-3.9367<br/>[-4.2074, -3.7744]","-3.9886<br/>[-4.3565, -3.7597]","-4.0355<br/>[-4.3220, -3.8592]","-3.9702<br/>[-4.4674, -3.7234]","-4.0435<br/>[-4.3078, -3.8659]","-4.0750<br/>[-4.3664, -3.8620]","-4.0635<br/>[-4.4387, -3.8362]","-4.0423<br/>[-4.5562, -3.7894]","-4.0469<br/>[-4.5442, -3.7780]","-4.1254<br/>[-4.3857, -3.9379]","-4.1161<br/>[-4.5003, -3.9014]","-4.0970<br/>[-4.6457, -3.8148]","-4.7928<br/>[-5.6411, -4.3128]","-4.8326<br/>[-5.6826, -4.3513]","-4.8622<br/>[-5.7104, -4.3800]","-4.8545<br/>[-5.7000, -4.3758]","-4.8297<br/>[-5.6427, -4.3432]","-4.7320<br/>[-5.3872, -4.2901]","-4.4328<br/>[-5.0217, -4.0701]","-5.0474<br/>[-5.8846, -4.5675]","-4.8748<br/>[-5.6921, -4.4052]","-4.8459<br/>[-5.6377, -4.3826]","-4.9339<br/>[-5.7433, -4.4634]","-4.9691<br/>[-5.7677, -4.4985]","-4.6550<br/>[-5.2129, -4.2673]","-4.8136<br/>[-5.5349, -4.3826]","-4.9500<br/>[-5.7181, -4.4991]","-4.9551<br/>[-5.7420, -4.4911]","-4.9351<br/>[-5.6382, -4.4847]","-4.9711<br/>[-5.7094, -4.5253]","-4.6979<br/>[-5.2369, -4.3206]","-5.0429<br/>[-5.7791, -4.5983]","-5.0614<br/>[-5.8028, -4.6175]","-4.8688<br/>[-5.5860, -4.4365]","-5.0437<br/>[-5.7430, -4.5961]","-5.0360<br/>[-5.7687, -4.5919]","-4.9925<br/>[-5.7074, -4.5568]","-5.0747<br/>[-5.7921, -4.6359]","-4.9948<br/>[-5.6975, -4.5673]","-5.0151<br/>[-5.7243, -4.5833]","-4.9824<br/>[-5.6431, -4.5523]","-5.0757<br/>[-5.7858, -4.6411]","-5.0154<br/>[-5.7006, -4.5914]","-5.0883<br/>[-5.7322, -4.6613]"]],"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":[["1","8","19","6","3","20","17","18","10","12","13","15","7","14","16","2","4","9","11","5"],[7110,9814,5639,8469,9683,7768,8090,6992,7969,6948,7269,7404,7902,9075,9853,8546,11960,9199,9984,11068],[264.994762896991,38.305747729592,0.263633244817549,0.11703346755123,0.0967231633223274,-0.0745887541714472,-0.344949698565704,-0.409900624345097,-0.4305165883297,-0.445390217378468,-0.448570740905939,-0.45394431187495,-0.472311184950118,-0.479378179795713,-0.482373007786294,-0.486653783734124,-0.492487997126085,-0.496576896060582,-0.515804245194279,-0.536491112981671],["-4.6335<br/>[-4.7093, -4.5551]","-4.5975<br/>[-4.6671, -4.5246]","-4.6157<br/>[-4.6884, -4.5399]","-4.6149<br/>[-4.6875, -4.5393]","-4.6145<br/>[-4.6866, -4.5392]","-4.6070<br/>[-4.6758, -4.5343]","-4.5995<br/>[-4.6689, -4.5272]","-4.5989<br/>[-4.6685, -4.5260]","-4.5985<br/>[-4.6680, -4.5256]","-4.5982<br/>[-4.6680, -4.5252]","-4.5982<br/>[-4.6679, -4.5252]","-4.5982<br/>[-4.6678, -4.5251]","-4.5979<br/>[-4.6676, -4.5248]","-4.5978<br/>[-4.6674, -4.5249]","-4.5974<br/>[-4.6670, -4.5245]","-4.5976<br/>[-4.6673, -4.5246]","-4.5977<br/>[-4.6670, -4.5251]","-4.5975<br/>[-4.6671, -4.5245]","-4.5972<br/>[-4.6668, -4.5241]","-4.5968<br/>[-4.6664, -4.5238]"],["-3.1352<br/>[-3.1458, -3.1240]","-3.6056<br/>[-3.6833, -3.5153]","-3.6655<br/>[-3.7452, -3.5448]","-3.8106<br/>[-3.9157, -3.6688]","-3.8232<br/>[-3.9781, -3.6414]","-3.8982<br/>[-4.1918, -3.7207]","-4.2108<br/>[-4.9401, -3.8457]","-4.5315<br/>[-5.2711, -4.0894]","-4.5313<br/>[-5.3432, -4.0786]","-4.8734<br/>[-5.6826, -4.3992]","-4.8131<br/>[-5.6140, -4.3434]","-4.8440<br/>[-5.6750, -4.3788]","-4.9487<br/>[-5.7357, -4.4803]","-4.7504<br/>[-5.4938, -4.3037]","-4.6638<br/>[-5.3875, -4.2216]","-4.9576<br/>[-5.7246, -4.4964]","-4.5485<br/>[-5.2339, -4.1221]","-4.9121<br/>[-5.6994, -4.4607]","-4.9733<br/>[-5.7432, -4.5268]","-4.9949<br/>[-5.7058, -4.5533]"]],"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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