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<h1 class="title toc-ignore">Enrichment results of ulcerative colitis</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/26192919">“Association Analyses Identify 38 Susceptibility Loci for Inflammatory Bowel Disease and Highlight Shared Genetic Risk Across Populations” (<em>Nature Genetics</em>, 2015)</a>. The summary data file is available at <a href="https://www.ibdgenetics.org/downloads.html" class="uri">https://www.ibdgenetics.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>
<script type="application/json" data-for="htmlwidget-983860bb2d7d6ad3a872">{"x":{"filter":"none","data":[["Inflammatory bowel disease (IBD)<br/>(3131, kegg, BioSystems)","Cytokine-cytokine receptor interaction<br/>(3850, kegg, BioSystems)","IL23-mediated signaling events<br/>(2641, pid, PC)","IL27-mediated signaling events<br/>(2201, pid, PC)","Allograft rejection<br/>(2583, kegg, BioSystems)","Toxoplasmosis<br/>(3604, kegg, BioSystems)","Leishmaniasis<br/>(3253, kegg, BioSystems)","Tuberculosis<br/>(3762, kegg, BioSystems)","Allograft Rejection<br/>(2604, wiki, BioSystems)","IL12-mediated signaling events<br/>(3106, pid, PC)","IL12-mediated signaling events<br/>(3122, pid, BioSystems)","Jak-STAT signaling pathway<br/>(3722, kegg, BioSystems)","Cytokine Signaling in Immune system<br/>(3867, reactome, PC)","Selective expression of chemokine receptors during T-cell polarization<br/>(2258, biocarta, BioCarta)","Cytokines and Inflammatory Response<br/>(2305, biocarta, BioCarta)","Th1/Th2 Differentiation<br/>(1794, biocarta, BioCarta)","IL12 and Stat4 Dependent Signaling Pathway in Th1 Development<br/>(1904, biocarta, BioCarta)","Herpes simplex infection<br/>(3768, kegg, BioSystems)","Interferon gamma signaling<br/>(3228, reactome, PC)","NO2-dependent IL 12 Pathway in NK cells<br/>(1659, biocarta, BioCarta)","IL2-mediated signaling events<br/>(2993, pid, BioSystems)","Interferon gamma signaling<br/>(3462, reactome, BioSystems)","IL2-mediated signaling events<br/>(3019, pid, PC)","Measles<br/>(3658, kegg, BioSystems)","Cytokines and Inflammatory Response<br/>(2183, wiki, BioSystems)","IFN-gamma pathway<br/>(2796, pid, PC)","IFN-gamma pathway<br/>(2740, pid, BioSystems)","Intestinal immune network for IgA production<br/>(2841, kegg, BioSystems)","Interferon Signaling<br/>(3794, reactome, BioSystems)","Leptin signaling pathway<br/>(3099, wiki, BioSystems)","Cytokine Network<br/>(1901, biocarta, BioCarta)","Delta-Notch Signaling Pathway<br/>(3405, wiki, BioSystems)","Costimulation by the CD28 family<br/>(3198, reactome, PC)","Pertussis<br/>(3312, kegg, BioSystems)","Interferon Signaling<br/>(3752, reactome, PC)","Signaling events mediated by PTP1B<br/>(3003, pid, PC)","Staphylococcus aureus infection<br/>(3032, kegg, BioSystems)","Notch signaling pathway<br/>(2927, kegg, BioSystems)","Signaling events mediated by TCPTP<br/>(2724, pid, PC)","Type I diabetes mellitus<br/>(2767, kegg, BioSystems)","Dendritic cells in regulating TH1 and TH2 Development<br/>(1955, biocarta, BioCarta)","Pathways in cancer<br/>(3904, kegg, BioSystems)","IL12 signaling mediated by STAT4<br/>(2321, pid, BioSystems)","IL 18 Signaling Pathway<br/>(734, biocarta, BioCarta)","TSLP Signaling Pathway<br/>(2659, wiki, BioSystems)","TNFs bind their physiological receptors<br/>(2091, reactome, BioSystems)","NOD pathway<br/>(2663, wiki, BioSystems)","Influenza A<br/>(3751, kegg, BioSystems)","Signaling events mediated by PTP1B<br/>(2975, pid, BioSystems)","Interleukin signaling pathway<br/>(3333, panther, PANTHER)","Graft-versus-host disease<br/>(2710, kegg, BioSystems)","HTLV-I infection<br/>(3846, kegg, BioSystems)","IL12 signaling mediated by STAT4<br/>(2376, pid, PC)","Autoimmune thyroid disease<br/>(2955, kegg, BioSystems)","S1P3 pathway<br/>(2165, pid, PC)","glycine cleavage<br/>(266, humancyc, PC)","IL6-mediated signaling events<br/>(2790, pid, BioSystems)","Multifunctional anion exchangers<br/>(744, reactome, BioSystems)","Signaling by Interleukins<br/>(3563, reactome, PC)","Epstein-Barr virus infection<br/>(3798, kegg, BioSystems)","Interleukin signaling pathway<br/>(3379, panther, PC)","Notch Signaling Pathway<br/>(2874, wiki, BioSystems)","B Cell Receptor Signaling Pathway<br/>(3731, wiki, BioSystems)","Catecholamine biosynthesis<br/>(364, reactome, PC)","Prolactin Signaling Pathway<br/>(3303, wiki, BioSystems)","Signaling events mediated by TCPTP<br/>(2632, pid, BioSystems)","Multifunctional anion exchangers<br/>(807, reactome, PC)","Inflammatory Response Pathway<br/>(2316, wiki, BioSystems)","Angiogenesis<br/>(3676, panther, PANTHER)","IL22 Soluble Receptor Signaling Pathway <br/>(1657, biocarta, BioCarta)","Angiogenesis<br/>(3701, panther, PC)","Type II interferon signaling (IFNG)<br/>(2952, wiki, BioSystems)","Catecholamine biosynthesis, tyrosine => dopamine => noradrenaline => adrenaline<br/>(635, kegg, BioSystems)","HIF-1 signaling pathway<br/>(3522, kegg, BioSystems)","NOD-like receptor signaling pathway<br/>(3062, kegg, BioSystems)","NOTCH2 intracellular domain regulates transcription<br/>(1231, reactome, PC)","Signaling by NOTCH2<br/>(2445, reactome, BioSystems)","S1P3 pathway<br/>(2318, pid, BioSystems)","Signaling by NOTCH2<br/>(2390, reactome, PC)","Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways<br/>(2888, reactome, PC)","PDGFR-beta signaling pathway<br/>(3646, pid, PC)","catecholamine biosynthesis<br/>(166, biocyc, BioSystems)","Asthma<br/>(2271, kegg, BioSystems)","Antigen processing and presentation<br/>(3313, kegg, BioSystems)","SHP2 signaling<br/>(3083, pid, PC)","IL-10 Anti-inflammatory Signaling Pathway<br/>(1724, biocarta, BioCarta)","catecholamine biosynthesis<br/>(258, humancyc, PC)","Biogenic Amine Synthesis<br/>(1454, wiki, BioSystems)","IL6-mediated signaling events<br/>(2867, pid, PC)","Notch signaling pathway<br/>(2653, panther, PANTHER)","IL-5 Signaling Pathway<br/>(3235, wiki, BioSystems)","AGE/RAGE pathway<br/>(3187, wiki, BioSystems)","Interferon alpha/beta signaling<br/>(3202, reactome, PC)","TGF-beta Receptor Signaling Pathway<br/>(3725, wiki, BioSystems)","Legionellosis<br/>(3057, kegg, BioSystems)","noradrenaline and adrenaline degradation<br/>(983, biocyc, BioSystems)","Interferon alpha/beta signaling<br/>(3249, reactome, BioSystems)","IL-3 Signaling Pathway<br/>(3524, wiki, BioSystems)","Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants<br/>(3027, reactome, BioSystems)"],[61,253,37,26,34,111,68,171,35,59,60,148,272,27,28,18,20,174,67,16,51,89,53,127,25,43,40,44,192,58,20,83,65,74,166,52,53,48,40,41,21,385,28,6,37,23,37,165,50,77,39,250,30,49,25,3,42,6,103,195,81,46,153,4,73,36,7,28,132,16,138,49,5,98,55,11,31,28,30,47,123,2,27,74,57,17,3,13,46,37,67,64,65,149,55,8,68,98,53],[4655,16833,3010,2010,1527,9480,4590,12371,1483,4506,4506,10495,21562,1973,1740,1598,1898,11897,4588,1371,5354,6373,5515,9756,2425,4363,4067,2707,13486,5249,1616,7974,4767,5164,11395,4942,2423,4236,3660,2584,1628,41508,2287,517,3048,1643,3170,11818,4736,6682,1470,19994,2519,2307,2435,323,3633,578,10179,15159,6926,3739,16629,449,6845,3279,609,2663,14035,1281,14669,3433,527,10222,4487,1262,3055,2708,2922,4164,12954,276,1234,2724,6620,1230,379,1383,4173,2986,6427,6239,3416,13572,3816,702,3632,9450,5586],[11.7777899156656,11.4659673959982,10.4039813633278,8.86137250459401,8.8234726681927,8.67489841540461,8.56670064544698,8.13907217961692,7.55147831869124,7.4891050422725,7.4891050422725,6.99573086760745,6.71626753388471,6.47822910865318,6.37162085871692,6.32780366282915,6.16254368187738,5.91750135014018,5.86631527361838,5.81703309505204,5.43032801943769,5.32333137460808,5.23217860233065,5.12816241897386,5.07053261889146,4.87385543813796,4.81121687001063,4.78750868235067,4.77120076363273,4.73966428471067,4.72038944018429,4.62246411857219,4.46340701448211,4.42974330771515,4.37504046906559,4.24432079612761,4.22993209481586,4.17178915857393,4.16800821605049,4.10886552206315,4.00822776481636,4.00418332161968,3.82439728781702,3.77425533275869,3.75800931374525,3.65259134459946,3.64466612247758,3.62499743610561,3.5914056076103,3.56820311020309,3.56735674858405,3.49373631357333,3.46861897552054,3.36303427701969,3.34668304053268,3.29905451281655,3.27794406355747,3.27319749065149,3.21708199912727,3.19784830707537,3.18794110411927,3.1784128311242,3.1690612329851,3.14140504300544,3.13867720398635,3.12767148052005,3.1195554731091,3.1150829617589,3.10652500112441,3.10274287409769,3.07426138308294,3.05972552630972,3.02757895614272,2.99480516172316,2.96501585742617,2.96058023232092,2.95126300842409,2.92023644212758,2.91127749903073,2.90263831030674,2.89148280406167,2.84140523119432,2.83956009954157,2.82899493672026,2.81849678949124,2.75214709159261,2.71312558826401,2.6961674521397,2.69333609105999,2.64188823484587,2.63999256356774,2.53908964759045,2.51176312168437,2.49566804964565,2.48208464880349,2.47793033052883,2.47546374664753,2.44155807837381,2.37465052739099],["-3.0627<br/>[-3.2121, -2.9765]","-3.0653<br/>[-3.2157, -2.9787]","-3.0617<br/>[-3.2108, -2.9756]","-3.0604<br/>[-3.2091, -2.9746]","-3.0601<br/>[-3.2087, -2.9743]","-3.0628<br/>[-3.2122, -2.9766]","-3.0618<br/>[-3.2110, -2.9757]","-3.0642<br/>[-3.2141, -2.9777]","-3.0601<br/>[-3.2086, -2.9742]","-3.0609<br/>[-3.2097, -2.9750]","-3.0609<br/>[-3.2097, -2.9750]","-3.0624<br/>[-3.2117, -2.9763]","-3.0630<br/>[-3.2126, -2.9768]","-3.0596<br/>[-3.2081, -2.9739]","-3.0596<br/>[-3.2081, -2.9739]","-3.0596<br/>[-3.2080, -2.9738]","-3.0600<br/>[-3.2085, -2.9742]","-3.0615<br/>[-3.2103, -2.9756]","-3.0609<br/>[-3.2098, -2.9750]","-3.0597<br/>[-3.2083, -2.9740]","-3.0609<br/>[-3.2099, -2.9749]","-3.0610<br/>[-3.2099, -2.9750]","-3.0609<br/>[-3.2099, -2.9749]","-3.0617<br/>[-3.2110, -2.9757]","-3.0596<br/>[-3.2080, -2.9738]","-3.0602<br/>[-3.2088, -2.9744]","-3.0602<br/>[-3.2087, -2.9744]","-3.0593<br/>[-3.2077, -2.9736]","-3.0612<br/>[-3.2101, -2.9752]","-3.0609<br/>[-3.2100, -2.9749]","-3.0595<br/>[-3.2080, -2.9738]","-3.0605<br/>[-3.2092, -2.9747]","-3.0596<br/>[-3.2082, -2.9739]","-3.0607<br/>[-3.2094, -2.9748]","-3.0609<br/>[-3.2097, -2.9750]","-3.0608<br/>[-3.2100, -2.9749]","-3.0598<br/>[-3.2083, -2.9740]","-3.0594<br/>[-3.2077, -2.9737]","-3.0597<br/>[-3.2079, -2.9740]","-3.0595<br/>[-3.2078, -2.9737]","-3.0595<br/>[-3.2080, -2.9738]","-3.0642<br/>[-3.2137, -2.9780]","-3.0591<br/>[-3.2073, -2.9735]","-3.0587<br/>[-3.2069, -2.9731]","-3.0594<br/>[-3.2077, -2.9738]","-3.0590<br/>[-3.2074, -2.9733]","-3.0591<br/>[-3.2073, -2.9735]","-3.0615<br/>[-3.2105, -2.9756]","-3.0605<br/>[-3.2096, -2.9746]","-3.0599<br/>[-3.2084, -2.9741]","-3.0588<br/>[-3.2069, -2.9732]","-3.0615<br/>[-3.2102, -2.9755]","-3.0591<br/>[-3.2073, -2.9735]","-3.0588<br/>[-3.2070, -2.9732]","-3.0599<br/>[-3.2086, -2.9741]","-3.0590<br/>[-3.2073, -2.9733]","-3.0591<br/>[-3.2073, -2.9735]","-3.0585<br/>[-3.2066, -2.9729]","-3.0603<br/>[-3.2090, -2.9745]","-3.0612<br/>[-3.2100, -2.9753]","-3.0599<br/>[-3.2084, -2.9741]","-3.0586<br/>[-3.2067, -2.9731]","-3.0619<br/>[-3.2112, -2.9757]","-3.0575<br/>[-3.2053, -2.9721]","-3.0602<br/>[-3.2090, -2.9744]","-3.0592<br/>[-3.2074, -2.9736]","-3.0585<br/>[-3.2066, -2.9729]","-3.0589<br/>[-3.2070, -2.9732]","-3.0612<br/>[-3.2100, -2.9752]","-3.0585<br/>[-3.2065, -2.9730]","-3.0612<br/>[-3.2101, -2.9753]","-3.0595<br/>[-3.2079, -2.9737]","-3.0575<br/>[-3.2053, -2.9721]","-3.0607<br/>[-3.2094, -2.9748]","-3.0586<br/>[-3.2067, -2.9731]","-3.0588<br/>[-3.2070, -2.9731]","-3.0591<br/>[-3.2074, -2.9734]","-3.0597<br/>[-3.2083, -2.9739]","-3.0591<br/>[-3.2073, -2.9734]","-3.0587<br/>[-3.2068, -2.9731]","-3.0611<br/>[-3.2100, -2.9751]","-3.0574<br/>[-3.2052, -2.9720]","-3.0586<br/>[-3.2067, -2.9730]","-3.0596<br/>[-3.2081, -2.9739]","-3.0603<br/>[-3.2089, -2.9744]","-3.0587<br/>[-3.2068, -2.9731]","-3.0574<br/>[-3.2052, -2.9720]","-3.0576<br/>[-3.2054, -2.9721]","-3.0591<br/>[-3.2072, -2.9735]","-3.0584<br/>[-3.2064, -2.9728]","-3.0595<br/>[-3.2077, -2.9738]","-3.0598<br/>[-3.2081, -2.9740]","-3.0593<br/>[-3.2076, -2.9736]","-3.0602<br/>[-3.2086, -2.9745]","-3.0596<br/>[-3.2081, -2.9739]","-3.0574<br/>[-3.2051, -2.9719]","-3.0593<br/>[-3.2076, -2.9736]","-3.0601<br/>[-3.2088, -2.9743]","-3.0592<br/>[-3.2075, -2.9735]"],["-1.8925<br/>[-2.0457, -1.7687]","-2.1890<br/>[-2.3488, -2.0365]","-1.7933<br/>[-1.9759, -1.6583]","-1.7478<br/>[-1.9332, -1.6131]","-1.6483<br/>[-1.8037, -1.5266]","-2.0895<br/>[-2.2329, -1.9774]","-1.9319<br/>[-2.0717, -1.8153]","-2.1952<br/>[-2.3357, -2.0909]","-1.6798<br/>[-1.8549, -1.5536]","-2.0256<br/>[-2.2166, -1.8937]","-2.0256<br/>[-2.2166, -1.8937]","-2.1841<br/>[-2.3708, -2.0304]","-2.3331<br/>[-2.4715, -2.2193]","-1.8545<br/>[-2.0609, -1.7058]","-1.7987<br/>[-1.9804, -1.6704]","-1.8021<br/>[-2.0081, -1.6473]","-1.8356<br/>[-2.0414, -1.6773]","-2.1626<br/>[-2.2794, -2.0699]","-2.0432<br/>[-2.2151, -1.9221]","-1.7713<br/>[-1.9861, -1.6080]","-2.0762<br/>[-2.2518, -1.9406]","-2.1306<br/>[-2.3041, -2.0025]","-2.0930<br/>[-2.2757, -1.9626]","-2.2021<br/>[-2.3926, -2.0782]","-1.9465<br/>[-2.1233, -1.8107]","-2.0235<br/>[-2.2053, -1.8788]","-2.0150<br/>[-2.2046, -1.8730]","-1.9253<br/>[-2.1074, -1.7787]","-2.3066<br/>[-2.4689, -2.1812]","-2.0643<br/>[-2.2114, -1.9508]","-1.8533<br/>[-2.0629, -1.7167]","-2.1768<br/>[-2.2618, -2.0613]","-2.1352<br/>[-2.2380, -2.0232]","-2.1033<br/>[-2.2929, -1.9678]","-2.2969<br/>[-2.4807, -2.1722]","-2.1269<br/>[-2.3163, -1.9862]","-1.9438<br/>[-2.1520, -1.7978]","-2.1503<br/>[-2.2607, -2.0203]","-1.9877<br/>[-2.2098, -1.8395]","-1.9707<br/>[-2.1743, -1.8215]","-1.8775<br/>[-2.1069, -1.7269]","-2.6350<br/>[-2.8132, -2.5132]","-1.9128<br/>[-2.1406, -1.7532]","-1.5925<br/>[-1.8471, -1.4239]","-1.9620<br/>[-2.1907, -1.8035]","-2.0461<br/>[-2.3445, -1.8586]","-2.1840<br/>[-2.5459, -1.9996]","-2.3004<br/>[-2.4960, -2.1612]","-2.1505<br/>[-2.3565, -2.0034]","-2.2721<br/>[-2.4961, -2.1157]","-1.8504<br/>[-2.0851, -1.6934]","-2.4016<br/>[-2.5696, -2.2693]","-1.9593<br/>[-2.2059, -1.7999]","-1.9803<br/>[-2.2158, -1.8325]","-2.0345<br/>[-2.2542, -1.8845]","-1.5590<br/>[-1.8215, -1.3863]","-2.0170<br/>[-2.2732, -1.8525]","-1.6732<br/>[-1.9171, -1.4992]","-2.2853<br/>[-2.4951, -2.1357]","-2.3768<br/>[-2.5720, -2.2425]","-2.2904<br/>[-2.5283, -2.1202]","-2.1659<br/>[-2.3057, -2.0268]","-2.3585<br/>[-2.5478, -2.2183]","-2.0344<br/>[-2.4697, -1.7764]","-2.2117<br/>[-2.4584, -2.0653]","-2.0215<br/>[-2.2542, -1.8522]","-1.6998<br/>[-1.9632, -1.5309]","-2.0397<br/>[-2.2829, -1.8764]","-2.3743<br/>[-2.5525, -2.2293]","-1.7907<br/>[-2.0665, -1.6091]","-2.3817<br/>[-2.5730, -2.2448]","-2.0887<br/>[-2.3247, -1.9325]","-2.1057<br/>[-2.5211, -1.8412]","-2.2980<br/>[-2.5163, -2.1457]","-2.3085<br/>[-2.6725, -2.0973]","-2.1472<br/>[-2.4179, -1.9464]","-2.1886<br/>[-2.3284, -2.0421]","-2.0751<br/>[-2.3127, -1.9215]","-2.2048<br/>[-2.3421, -2.0521]","-2.3198<br/>[-2.7308, -2.1191]","-2.3545<br/>[-2.5489, -2.2074]","-2.1189<br/>[-2.3911, -1.8417]","-1.8431<br/>[-2.1273, -1.6704]","-2.0836<br/>[-2.3267, -1.9319]","-2.2387<br/>[-2.4834, -2.0880]","-1.7990<br/>[-2.1100, -1.6093]","-2.2365<br/>[-2.5105, -1.9537]","-2.3815<br/>[-2.7672, -2.1211]","-2.0944<br/>[-2.3801, -1.9253]","-2.2043<br/>[-2.3505, -2.0465]","-2.2137<br/>[-2.4880, -2.0588]","-2.2268<br/>[-2.4868, -2.0668]","-2.1383<br/>[-2.4156, -1.9769]","-2.3785<br/>[-2.5973, -2.2296]","-2.1883<br/>[-2.4276, -2.0293]","-2.4465<br/>[-2.7196, -2.1686]","-2.1494<br/>[-2.4115, -1.9805]","-2.2997<br/>[-2.5387, -2.1349]","-2.2403<br/>[-2.3769, -2.1083]"]],"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":[["Heart - Atrial Appendage","Artery - Coronary","Small Intestine - Terminal Ileum","Muscle - Skeletal","Heart - Left Ventricle","Colon - Transverse","Whole Blood","Testis","Brain - Anterior cingulate cortex (BA24)","Spleen","Brain - Cerebellum","Lung","Brain - Cerebellar Hemisphere","Adipose - Subcutaneous","Adipose - Visceral (Omentum)","Thyroid","Brain - Cortex","Nerve - Tibial","Brain - Frontal Cortex (BA9)","Brain - Caudate (basal ganglia)","Adrenal Gland","Vagina","Esophagus - Muscularis","Breast - Mammary Tissue","Colon - Sigmoid","Esophagus - Gastroesophageal Junction","Pancreas","Artery - Tibial","Uterus","Stomach","Brain - Nucleus accumbens (basal ganglia)","Cells - Transformed fibroblasts","Prostate","Brain - Hypothalamus","Brain - Hippocampus","Ovary","Artery - Aorta","Brain - Putamen (basal ganglia)","Esophagus - Mucosa","Cells - EBV-transformed lymphocytes","Skin - Not Sun Exposed (Suprapubic)","Pituitary","Skin - Sun Exposed (Lower leg)","Liver"],[5835,6339,4823,5894,5811,5499,5883,6008,5912,4050,5679,5037,5677,5731,5907,6370,5821,5790,6220,6529,5740,5957,6149,5737,6116,6015,5276,6215,5858,5449,6221,6289,5756,5929,5799,6021,6539,6620,5786,5223,5959,5997,5965,6510],[6.94957196045773,3.89260420996516,3.85709494054574,3.53669648030069,1.98001862984312,0.370866404807422,0.249025195971906,-0.0257305532920641,-0.0789514497767635,-0.125240633172153,-0.130023452880979,-0.191423379416725,-0.204295714356796,-0.259775401318598,-0.367473367430902,-0.387549795651008,-0.420702737720644,-0.461563743791422,-0.462149132691812,-0.482476239112687,-0.499460489216303,-0.504184650143575,-0.511227827293686,-0.519569646432576,-0.523832043273849,-0.530360189332404,-0.548401138260268,-0.559275365310073,-0.588704053127681,-0.601572229038269,-0.606912671718269,-0.617178434276452,-0.634417586540707,-0.645922389276553,-0.647634702340871,-0.647697890986718,-0.676254354855349,-0.682967398443419,-0.755112398370179,-0.759675978619486,-0.774951659730574,-0.78348114412622,-0.808727811064362,-0.96663541207374],["-3.0574<br/>[-3.2051, -2.9720]","-3.0578<br/>[-3.2056, -2.9723]","-3.0575<br/>[-3.2053, -2.9721]","-3.0586<br/>[-3.2067, -2.9731]","-3.0579<br/>[-3.2058, -2.9725]","-3.0585<br/>[-3.2067, -2.9729]","-3.0586<br/>[-3.2067, -2.9730]","-3.0581<br/>[-3.2059, -2.9726]","-3.0580<br/>[-3.2058, -2.9725]","-3.0582<br/>[-3.2061, -2.9726]","-3.0579<br/>[-3.2058, -2.9725]","-3.0581<br/>[-3.2061, -2.9726]","-3.0579<br/>[-3.2057, -2.9724]","-3.0579<br/>[-3.2057, -2.9725]","-3.0579<br/>[-3.2057, -2.9724]","-3.0579<br/>[-3.2058, -2.9725]","-3.0576<br/>[-3.2054, -2.9722]","-3.0578<br/>[-3.2056, -2.9724]","-3.0576<br/>[-3.2054, -2.9722]","-3.0578<br/>[-3.2056, -2.9723]","-3.0579<br/>[-3.2058, -2.9724]","-3.0578<br/>[-3.2056, -2.9723]","-3.0578<br/>[-3.2056, -2.9723]","-3.0577<br/>[-3.2055, -2.9723]","-3.0578<br/>[-3.2056, -2.9723]","-3.0578<br/>[-3.2056, -2.9723]","-3.0577<br/>[-3.2055, -2.9722]","-3.0578<br/>[-3.2056, -2.9723]","-3.0577<br/>[-3.2055, -2.9722]","-3.0577<br/>[-3.2055, -2.9722]","-3.0576<br/>[-3.2054, -2.9722]","-3.0577<br/>[-3.2054, -2.9722]","-3.0576<br/>[-3.2054, -2.9722]","-3.0577<br/>[-3.2055, -2.9722]","-3.0576<br/>[-3.2053, -2.9722]","-3.0576<br/>[-3.2054, -2.9722]","-3.0576<br/>[-3.2054, -2.9722]","-3.0575<br/>[-3.2052, -2.9721]","-3.0574<br/>[-3.2052, -2.9720]","-3.0575<br/>[-3.2052, -2.9720]","-3.0574<br/>[-3.2052, -2.9720]","-3.0574<br/>[-3.2052, -2.9720]","-3.0574<br/>[-3.2052, -2.9720]","-3.0570<br/>[-3.2047, -2.9717]"],["-2.1787<br/>[-2.2947, -2.0894]","-2.2284<br/>[-2.3960, -2.1217]","-2.2596<br/>[-2.4521, -2.1432]","-2.2361<br/>[-2.3664, -2.1092]","-2.3152<br/>[-2.5458, -2.1871]","-2.4981<br/>[-2.8313, -2.2944]","-2.5174<br/>[-2.8629, -2.3098]","-2.5672<br/>[-2.9169, -2.3504]","-2.5664<br/>[-2.9424, -2.3380]","-2.5574<br/>[-2.9116, -2.3191]","-2.5792<br/>[-2.9500, -2.3531]","-2.5931<br/>[-2.9370, -2.3551]","-2.6048<br/>[-2.9577, -2.3768]","-2.6023<br/>[-2.9745, -2.3503]","-2.6488<br/>[-2.9940, -2.4016]","-2.6612<br/>[-2.9919, -2.4141]","-2.6738<br/>[-2.9940, -2.4292]","-2.6832<br/>[-3.0042, -2.4278]","-2.6927<br/>[-3.0025, -2.4485]","-2.7089<br/>[-3.0013, -2.4738]","-2.7193<br/>[-2.9902, -2.4870]","-2.7040<br/>[-3.0108, -2.4510]","-2.7106<br/>[-3.0108, -2.4611]","-2.7095<br/>[-3.0138, -2.4538]","-2.7158<br/>[-3.0130, -2.4689]","-2.7189<br/>[-3.0136, -2.4717]","-2.7300<br/>[-3.0115, -2.4855]","-2.7309<br/>[-3.0206, -2.4825]","-2.7452<br/>[-3.0256, -2.4975]","-2.7501<br/>[-3.0294, -2.5015]","-2.7616<br/>[-3.0222, -2.5289]","-2.7601<br/>[-3.0308, -2.5173]","-2.7657<br/>[-3.0374, -2.5188]","-2.7732<br/>[-3.0386, -2.5306]","-2.7691<br/>[-3.0447, -2.5181]","-2.7741<br/>[-3.0384, -2.5304]","-2.7865<br/>[-3.0450, -2.5425]","-2.7884<br/>[-3.0486, -2.5433]","-2.8308<br/>[-3.0679, -2.5933]","-2.8390<br/>[-3.0720, -2.6030]","-2.8407<br/>[-3.0748, -2.6055]","-2.8465<br/>[-3.0739, -2.6155]","-2.8613<br/>[-3.0843, -2.6320]","-2.9514<br/>[-3.1500, -2.7267]"]],"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":[["Pancreas","Colon_Transverse","Spleen","Artery_Coronary","Testis","Whole_Blood","Skin_Not_Sun_Exposed_(Suprapubic)","Skin_Sun_Exposed_(Lower_leg)","Kidney_Cortex","Small_Intestine_Terminal_Ileum","Cells_EBV-transformed_lymphocytes","Minor_Salivary_Gland","Heart_Left_Ventricle","Brain_Caudate_(basal_ganglia)","Lung","Brain_Hippocampus","Heart_Atrial_Appendage","Brain_Frontal_Cortex_(BA9)","Colon_Sigmoid","Muscle_Skeletal","Brain_Cortex","Adipose_Visceral_(Omentum)","Brain_Putamen_(basal_ganglia)","Brain_Amygdala","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Anterior_cingulate_cortex_(BA24)","Esophagus_Mucosa","Ovary","Uterus","Nerve_Tibial","Pituitary","Prostate","Esophagus_Gastroesophageal_Junction","Stomach","Vagina","Liver","Brain_Cerebellum","Adipose_Subcutaneous","Esophagus_Muscularis","Brain_Substantia_nigra","Brain_Hypothalamus","Breast_Mammary_Tissue","Cells_Transformed_fibroblasts","Adrenal_Gland","Brain_Cerebellar_Hemisphere","Artery_Tibial","Thyroid","Brain_Spinal_cord_(cervical_c-1)","Artery_Aorta"],[7852,7839,7170,12422,8294,6984,6952,6862,9180,8873,7800,8485,11199,11859,8362,11048,11210,13643,10923,8851,12005,9627,11929,11272,11439,13027,7021,11628,12378,12564,9600,9368,14202,9433,6938,8565,10865,10040,14389,12721,12226,9928,11042,12662,13542,12748,12303,12621,14425],[3.29695800417448,1.59443932612298,1.40566019643265,1.04924259094405,0.910521862612333,0.459262987084611,0.416849309631466,0.382039401200209,0.348620125968072,0.068043455680345,0.0620342027144178,-0.209498647030777,-0.297491159608215,-0.328719377804746,-0.339903595520771,-0.384332031541813,-0.43860445072833,-0.447787902817847,-0.459273192344563,-0.515648223034951,-0.538823570045052,-0.586588925237926,-0.615082127513341,-0.62245483726933,-0.628120444506337,-0.641101556575835,-0.727853961812706,-0.768172244472477,-0.771028267357363,-0.798577582907887,-0.82133499389847,-0.826681565453154,-0.839149057846129,-0.872060164466877,-0.90543320715879,-0.913594805042535,-0.920161782668249,-0.940521133948663,-0.976545735436335,-0.990181269005605,-0.996410908089198,-1.00411929004868,-1.0041664963282,-1.02622599589007,-1.06538929285051,-1.07692646226631,-1.08371786033725,-1.12909922998004,-1.17732945904472],["-3.0604<br/>[-3.2093, -2.9745]","-3.0596<br/>[-3.2081, -2.9739]","-3.0591<br/>[-3.2073, -2.9735]","-3.0572<br/>[-3.2048, -2.9718]","-3.0589<br/>[-3.2070, -2.9733]","-3.0588<br/>[-3.2069, -2.9732]","-3.0571<br/>[-3.2048, -2.9717]","-3.0571<br/>[-3.2048, -2.9717]","-3.0592<br/>[-3.2077, -2.9735]","-3.0588<br/>[-3.2070, -2.9732]","-3.0581<br/>[-3.2060, -2.9726]","-3.0581<br/>[-3.2060, -2.9725]","-3.0570<br/>[-3.2046, -2.9717]","-3.0581<br/>[-3.2061, -2.9726]","-3.0582<br/>[-3.2060, -2.9727]","-3.0581<br/>[-3.2061, -2.9726]","-3.0569<br/>[-3.2045, -2.9716]","-3.0584<br/>[-3.2065, -2.9728]","-3.0586<br/>[-3.2067, -2.9730]","-3.0577<br/>[-3.2056, -2.9723]","-3.0580<br/>[-3.2060, -2.9725]","-3.0582<br/>[-3.2061, -2.9726]","-3.0576<br/>[-3.2055, -2.9722]","-3.0578<br/>[-3.2058, -2.9723]","-3.0580<br/>[-3.2059, -2.9724]","-3.0579<br/>[-3.2058, -2.9724]","-3.0578<br/>[-3.2057, -2.9723]","-3.0578<br/>[-3.2055, -2.9723]","-3.0580<br/>[-3.2058, -2.9725]","-3.0575<br/>[-3.2052, -2.9721]","-3.0578<br/>[-3.2056, -2.9723]","-3.0573<br/>[-3.2050, -2.9719]","-3.0581<br/>[-3.2061, -2.9726]","-3.0575<br/>[-3.2052, -2.9721]","-3.0573<br/>[-3.2051, -2.9719]","-3.0572<br/>[-3.2049, -2.9718]","-3.0575<br/>[-3.2053, -2.9720]","-3.0572<br/>[-3.2049, -2.9718]","-3.0578<br/>[-3.2056, -2.9723]","-3.0576<br/>[-3.2054, -2.9721]","-3.0570<br/>[-3.2048, -2.9716]","-3.0572<br/>[-3.2048, -2.9718]","-3.0574<br/>[-3.2050, -2.9720]","-3.0572<br/>[-3.2049, -2.9718]","-3.0572<br/>[-3.2049, -2.9718]","-3.0571<br/>[-3.2047, -2.9717]","-3.0572<br/>[-3.2050, -2.9718]","-3.0570<br/>[-3.2046, -2.9716]","-3.0569<br/>[-3.2045, -2.9716]"],["-2.0337<br/>[-2.1215, -1.9473]","-2.4034<br/>[-2.6708, -2.2328]","-2.3840<br/>[-2.6706, -2.2068]","-2.3765<br/>[-2.4035, -2.2836]","-2.5242<br/>[-2.8167, -2.3317]","-2.5079<br/>[-2.8552, -2.3210]","-2.8054<br/>[-3.0008, -2.6066]","-2.8213<br/>[-3.0070, -2.6246]","-2.4768<br/>[-2.8553, -2.1163]","-2.6013<br/>[-2.9177, -2.3974]","-2.6263<br/>[-2.9336, -2.4217]","-2.6552<br/>[-2.9527, -2.4502]","-2.6703<br/>[-3.0805, -2.4993]","-2.7261<br/>[-2.9658, -2.5434]","-2.6745<br/>[-2.9829, -2.4497]","-2.7364<br/>[-2.9681, -2.5518]","-2.7067<br/>[-3.0988, -2.5397]","-2.7702<br/>[-2.9759, -2.5990]","-2.7444<br/>[-2.9846, -2.5443]","-2.7521<br/>[-2.9900, -2.5469]","-2.7820<br/>[-2.9901, -2.5996]","-2.7809<br/>[-3.0014, -2.5936]","-2.7984<br/>[-3.0049, -2.6104]","-2.8076<br/>[-2.9961, -2.6304]","-2.8066<br/>[-3.0000, -2.6237]","-2.8128<br/>[-3.0081, -2.6352]","-2.8285<br/>[-3.0339, -2.6226]","-2.8312<br/>[-3.0576, -2.6228]","-2.8335<br/>[-3.0459, -2.6243]","-2.8519<br/>[-3.0423, -2.6600]","-2.8574<br/>[-3.0596, -2.6486]","-2.8602<br/>[-3.0625, -2.6512]","-2.8688<br/>[-3.0433, -2.6876]","-2.8779<br/>[-3.0782, -2.6654]","-2.9087<br/>[-3.1149, -2.6889]","-2.9022<br/>[-3.0984, -2.6934]","-2.9025<br/>[-3.0723, -2.7129]","-2.9072<br/>[-3.0957, -2.6998]","-2.9163<br/>[-3.0741, -2.7357]","-2.9263<br/>[-3.0837, -2.7446]","-2.9350<br/>[-3.0801, -2.7622]","-2.9415<br/>[-3.1154, -2.7421]","-2.9343<br/>[-3.1075, -2.7343]","-2.9424<br/>[-3.0973, -2.7646]","-2.9576<br/>[-3.1059, -2.7868]","-2.9636<br/>[-3.1157, -2.7801]","-2.9703<br/>[-3.1172, -2.7889]","-2.9907<br/>[-3.1385, -2.8105]","-3.0054<br/>[-3.1381, -2.8355]"]],"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":[["17","2","12","6","10","1","16","7","5","13","11","19","4","20","8","9","14","18","15","3"],[8328,9053,7279,9056,8579,7541,10146,8644,11513,7885,10547,5889,12453,8217,10470,9848,9558,7534,7843,10278],[1.58507322565543,1.29456671614697,1.01466815289904,0.500426642397829,0.391313729634571,0.387089099915889,0.0900496303944826,-0.176370247156216,-0.258835654798777,-0.318324711453963,-0.430371655434059,-0.522905862672428,-0.67764147555268,-0.706998394280296,-0.722713610300433,-0.73921021529491,-0.779289641521558,-0.791654680495339,-0.821969348582075,-0.838624067133741],["-3.0600<br/>[-3.2085, -2.9743]","-3.0597<br/>[-3.2083, -2.9739]","-3.0591<br/>[-3.2072, -2.9734]","-3.0585<br/>[-3.2066, -2.9729]","-3.0589<br/>[-3.2071, -2.9732]","-3.0585<br/>[-3.2066, -2.9730]","-3.0580<br/>[-3.2059, -2.9726]","-3.0584<br/>[-3.2064, -2.9729]","-3.0585<br/>[-3.2065, -2.9729]","-3.0582<br/>[-3.2059, -2.9727]","-3.0579<br/>[-3.2056, -2.9724]","-3.0578<br/>[-3.2057, -2.9723]","-3.0579<br/>[-3.2058, -2.9725]","-3.0571<br/>[-3.2047, -2.9718]","-3.0579<br/>[-3.2056, -2.9724]","-3.0578<br/>[-3.2056, -2.9723]","-3.0575<br/>[-3.2053, -2.9721]","-3.0574<br/>[-3.2052, -2.9720]","-3.0576<br/>[-3.2054, -2.9721]","-3.0574<br/>[-3.2052, -2.9720]"],["-2.3829<br/>[-2.6613, -2.2091]","-2.4435<br/>[-2.7000, -2.2758]","-2.4117<br/>[-2.7202, -2.2213]","-2.4392<br/>[-2.8480, -2.2855]","-2.5276<br/>[-2.8620, -2.3208]","-2.5043<br/>[-2.8739, -2.3063]","-2.5905<br/>[-2.9300, -2.3907]","-2.6491<br/>[-2.9506, -2.4432]","-2.6904<br/>[-2.9696, -2.4924]","-2.6278<br/>[-2.9395, -2.4161]","-2.7206<br/>[-2.9938, -2.5073]","-2.7343<br/>[-2.9907, -2.5057]","-2.8078<br/>[-3.0132, -2.6111]","-2.8102<br/>[-3.0352, -2.5903]","-2.8202<br/>[-3.0321, -2.6123]","-2.8243<br/>[-3.0381, -2.6118]","-2.8476<br/>[-3.0370, -2.6510]","-2.8425<br/>[-3.0714, -2.6139]","-2.8631<br/>[-3.0642, -2.6493]","-2.8604<br/>[-3.0652, -2.6462]"]],"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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