├── index_files ├── .DS_Store ├── bootstrap-3.3.5 │ ├── .DS_Store │ ├── css │ │ ├── .DS_Store │ │ ├── fonts │ │ │ ├── Lato.ttf │ │ │ ├── Raleway.ttf │ │ │ ├── Roboto.ttf │ │ │ ├── Ubuntu.ttf │ │ │ ├── LatoBold.ttf │ │ │ ├── LatoItalic.ttf │ │ │ ├── NewsCycle.ttf │ │ │ ├── OpenSans.ttf │ │ │ ├── RobotoBold.ttf │ │ │ ├── OpenSansBold.ttf │ │ │ ├── RalewayBold.ttf │ │ │ ├── RobotoLight.ttf │ │ │ ├── RobotoMedium.ttf │ │ │ ├── NewsCycleBold.ttf │ │ │ ├── OpenSansItalic.ttf │ │ │ ├── OpenSansLight.ttf │ │ │ ├── SourceSansPro.ttf │ │ │ ├── SourceSansProBold.ttf │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ ├── OpenSansLightItalic.ttf │ │ │ ├── SourceSansProItalic.ttf │ │ │ └── SourceSansProLight.ttf │ │ ├── bootstrap-theme.min.css │ │ └── bootstrap-theme.css │ ├── fonts │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 │ ├── js │ │ └── npm.js │ └── shim │ │ ├── html5shiv.min.js │ │ └── respond.min.js ├── crosstalk-1.2.1 │ ├── .DS_Store │ ├── css │ │ └── crosstalk.min.css │ ├── scss │ │ └── crosstalk.scss │ └── js │ │ └── crosstalk.min.js ├── dt-core-1.13.6 │ ├── .DS_Store │ └── css │ │ ├── jquery.dataTables.extra.css │ │ └── jquery.dataTables.min.css ├── dt-ext-buttons-1.13.6 │ ├── .DS_Store │ ├── js │ │ ├── buttons.print.min.js │ │ ├── buttons.colVis.min.js │ │ ├── buttons.html5.min.js │ │ └── dataTables.buttons.min.js │ └── css │ │ └── buttons.dataTables.min.css ├── navigation-1.1 │ ├── codefolding-lua.css │ ├── sourceembed.js │ ├── codefolding.js │ └── tabsets.js ├── highlightjs-9.12.0 │ ├── default.css │ └── textmate.css ├── header-attrs-2.29 │ └── header-attrs.js ├── htmltools-fill-0.5.8.1 │ └── fill.css ├── datatables-css-0.0.0 │ └── datatables-crosstalk.css ├── nouislider-7.0.10 │ ├── jquery.nouislider.min.css │ └── jquery.nouislider.min.js └── selectize-0.12.0 │ └── selectize.bootstrap3.css ├── README.md └── index.Rmd /index_files/.DS_Store: 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-------------------------------------------------------------------------------- /index_files/navigation-1.1/codefolding-lua.css: -------------------------------------------------------------------------------- 1 | detaiks.chunk-details > summary.chunk-summary { 2 | text-align: right; 3 | } 4 | details.chunk-details[open] > summary.chunk-summary::after { 5 | content: "Hide"; 6 | } 7 | details.chunk-details[open] > summary.chunk-summary > span.chunk-summary-text { 8 | display: none; 9 | } 10 | -------------------------------------------------------------------------------- /index_files/highlightjs-9.12.0/default.css: -------------------------------------------------------------------------------- 1 | .hljs-literal { 2 | color: #990073; 3 | } 4 | 5 | .hljs-number { 6 | color: #099; 7 | } 8 | 9 | .hljs-comment { 10 | color: #998; 11 | font-style: italic; 12 | } 13 | 14 | .hljs-keyword { 15 | color: #900; 16 | font-weight: bold; 17 | } 18 | 19 | .hljs-string { 20 | color: #d14; 21 | } 22 | -------------------------------------------------------------------------------- /index_files/highlightjs-9.12.0/textmate.css: -------------------------------------------------------------------------------- 1 | .hljs-literal { 2 | color: rgb(88, 72, 246); 3 | } 4 | 5 | .hljs-number { 6 | color: rgb(0, 0, 205); 7 | } 8 | 9 | .hljs-comment { 10 | color: rgb(76, 136, 107); 11 | } 12 | 13 | .hljs-keyword { 14 | color: rgb(0, 0, 255); 15 | } 16 | 17 | .hljs-string { 18 | color: rgb(3, 106, 7); 19 | } 20 | -------------------------------------------------------------------------------- /index_files/navigation-1.1/sourceembed.js: -------------------------------------------------------------------------------- 1 | 2 | window.initializeSourceEmbed = function(filename) { 3 | $("#rmd-download-source").click(function() { 4 | var src = $("#rmd-source-code").html(); 5 | var a = document.createElement('a'); 6 | a.href = "data:text/x-r-markdown;base64," + src; 7 | a.download = filename; 8 | document.body.appendChild(a); 9 | a.click(); 10 | document.body.removeChild(a); 11 | }); 12 | }; 13 | -------------------------------------------------------------------------------- /index_files/bootstrap-3.3.5/js/npm.js: -------------------------------------------------------------------------------- 1 | // This file is autogenerated via the `commonjs` Grunt task. You can require() this file in a CommonJS environment. 2 | require('../../js/transition.js') 3 | require('../../js/alert.js') 4 | require('../../js/button.js') 5 | require('../../js/carousel.js') 6 | require('../../js/collapse.js') 7 | require('../../js/dropdown.js') 8 | require('../../js/modal.js') 9 | require('../../js/tooltip.js') 10 | require('../../js/popover.js') 11 | require('../../js/scrollspy.js') 12 | require('../../js/tab.js') 13 | require('../../js/affix.js') -------------------------------------------------------------------------------- /index_files/header-attrs-2.29/header-attrs.js: -------------------------------------------------------------------------------- 1 | // Pandoc 2.9 adds attributes on both header and div. We remove the former (to 2 | // be compatible with the behavior of Pandoc < 2.8). 3 | document.addEventListener('DOMContentLoaded', function(e) { 4 | var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); 5 | var i, h, a; 6 | for (i = 0; i < hs.length; i++) { 7 | h = hs[i]; 8 | if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 9 | a = h.attributes; 10 | while (a.length > 0) h.removeAttribute(a[0].name); 11 | } 12 | }); 13 | -------------------------------------------------------------------------------- /index_files/htmltools-fill-0.5.8.1/fill.css: -------------------------------------------------------------------------------- 1 | @layer htmltools { 2 | .html-fill-container { 3 | display: flex; 4 | flex-direction: column; 5 | /* Prevent the container from expanding vertically or horizontally beyond its 6 | parent's constraints. */ 7 | min-height: 0; 8 | min-width: 0; 9 | } 10 | .html-fill-container > .html-fill-item { 11 | /* Fill items can grow and shrink freely within 12 | available vertical space in fillable container */ 13 | flex: 1 1 auto; 14 | min-height: 0; 15 | min-width: 0; 16 | } 17 | .html-fill-container > :not(.html-fill-item) { 18 | /* Prevent shrinking or growing of non-fill items */ 19 | flex: 0 0 auto; 20 | } 21 | } 22 | -------------------------------------------------------------------------------- /index_files/dt-core-1.13.6/css/jquery.dataTables.extra.css: -------------------------------------------------------------------------------- 1 | /* Selected rows/cells */ 2 | table.dataTable tr.selected td, table.dataTable td.selected { 3 | background-color: #b0bed9 !important; 4 | } 5 | /* In case of scrollX/Y or FixedHeader */ 6 | .dataTables_scrollBody .dataTables_sizing { 7 | visibility: hidden; 8 | } 9 | 10 | /* The datatables' theme CSS file doesn't define 11 | the color but with white background. It leads to an issue that 12 | when the HTML's body color is set to 'white', the user can't 13 | see the text since the background is white. One case happens in the 14 | RStudio's IDE when inline viewing the DT table inside an Rmd file, 15 | if the IDE theme is set to "Cobalt". 16 | 17 | See https://github.com/rstudio/DT/issues/447 for more info 18 | 19 | This fixes should have little side-effects because all the other elements 20 | of the default theme use the #333 font color. 21 | 22 | TODO: The upstream may use relative colors for both the table background 23 | and the color. It means the table can display well without this patch 24 | then. At that time, we need to remove the below CSS attributes. 25 | */ 26 | div.datatables { 27 | color: #333; 28 | } 29 | -------------------------------------------------------------------------------- /index_files/crosstalk-1.2.1/css/crosstalk.min.css: -------------------------------------------------------------------------------- 1 | .container-fluid.crosstalk-bscols{margin-left:-30px;margin-right:-30px;white-space:normal}body>.container-fluid.crosstalk-bscols{margin-left:auto;margin-right:auto}.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:inline-block;padding-right:12px;vertical-align:top}@media only screen and (max-width: 480px){.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:block;padding-right:inherit}}.crosstalk-input{margin-bottom:15px}.crosstalk-input .control-label{margin-bottom:0;vertical-align:middle}.crosstalk-input input[type="checkbox"]{margin:4px 0 0;margin-top:1px;line-height:normal}.crosstalk-input .checkbox{position:relative;display:block;margin-top:10px;margin-bottom:10px}.crosstalk-input .checkbox>label{padding-left:20px;margin-bottom:0;font-weight:400;cursor:pointer}.crosstalk-input .checkbox input[type="checkbox"],.crosstalk-input .checkbox-inline input[type="checkbox"]{position:absolute;margin-top:2px;margin-left:-20px}.crosstalk-input .checkbox+.checkbox{margin-top:-5px}.crosstalk-input .checkbox-inline{position:relative;display:inline-block;padding-left:20px;margin-bottom:0;font-weight:400;vertical-align:middle;cursor:pointer}.crosstalk-input .checkbox-inline+.checkbox-inline{margin-top:0;margin-left:10px} 2 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # [Genes4Epilepsy](https://bahlolab.github.io/Genes4Epilepsy/) 2 | A curated list of monogenic epilepsy genes. 3 | 4 | This list is actively maintained, and updates will be released twice yearly. 5 | 6 | The inclusion and exclusion criteria can be found here: [Oliver KL, et al. Genes4Epilepsy: An epilepsy gene resource. Epilepsia. 2023 May;64(5):1368-1375. doi: 10.1111/epi.17547. Epub 2023 Mar 9. PMID: 36808730](https://onlinelibrary.wiley.com/doi/10.1111/epi.17547) 7 | 8 | This publication has been recognized as a top cited article in Epilepsia. 9 | 10 | # [Interactive list and changelog](https://bahlolab.github.io/Genes4Epilepsy/) 11 | An interactive table and changelog showing all changes to the list since the original published version is available [here](https://bahlolab.github.io/Genes4Epilepsy/) 12 | 13 | # Download 14 | The latest version of the Genes4Epilepsy list can be accessed [here](https://github.com/bahlolab/Genes4Epilepsy/releases/latest) 15 | 16 | # Contact 17 | Suggestions for additions or updates to this list can be emailed to: genes4-epilepsy@unimelb.edu.au 18 | 19 | # Cite 20 | If you use this Genes4Epilepsy resource, please acknowledge by citing [Oliver KL, et al. Genes4Epilepsy: An epilepsy gene resource. Epilepsia. 2023 May;64(5):1368-1375. doi: 10.1111/epi.17547. Epub 2023 Mar 9. PMID: 36808730](https://onlinelibrary.wiley.com/doi/10.1111/epi.17547) 21 | -------------------------------------------------------------------------------- /index_files/datatables-css-0.0.0/datatables-crosstalk.css: -------------------------------------------------------------------------------- 1 | .dt-crosstalk-fade { 2 | opacity: 0.2; 3 | } 4 | 5 | html body div.DTS div.dataTables_scrollBody { 6 | background: none; 7 | } 8 | 9 | 10 | /* 11 | Fix https://github.com/rstudio/DT/issues/563 12 | If the `table.display` is set to "block" (e.g., pkgdown), the browser will display 13 | datatable objects strangely. The search panel and the page buttons will still be 14 | in full-width but the table body will be "compact" and shorter. 15 | In therory, having this attributes will affect `dom="t"` 16 | with `display: block` users. But in reality, there should be no one. 17 | We may remove the below lines in the future if the upstream agree to have this there. 18 | See https://github.com/DataTables/DataTablesSrc/issues/160 19 | */ 20 | 21 | table.dataTable { 22 | display: table; 23 | } 24 | 25 | 26 | /* 27 | When DTOutput(fill = TRUE), it receives a .html-fill-item class (via htmltools::bindFillRole()), which effectively amounts to `flex: 1 1 auto`. That's mostly fine, but the case where `fillContainer=TRUE`+`height:auto`+`flex-basis:auto` and the container (e.g., a bslib::card()) doesn't have a defined height is a bit problematic since the table wants to fit the parent but the parent wants to fit the table, which results pretty small table height (maybe because there is a minimum height somewhere?). It seems better in this case to impose a 400px height default for the table, which we can do by setting `flex-basis` to 400px (the table is still allowed to grow/shrink when the container has an opinionated height). 28 | */ 29 | 30 | .html-fill-container > .html-fill-item.datatables { 31 | flex-basis: 400px; 32 | } 33 | -------------------------------------------------------------------------------- /index_files/nouislider-7.0.10/jquery.nouislider.min.css: -------------------------------------------------------------------------------- 1 | /*! noUiSlider - 7.0.10 - 2015-03-17 17:30:22 */ 2 | 3 | 4 | .noUi-target,.noUi-target *{-webkit-touch-callout:none;-webkit-user-select:none;-ms-touch-action:none;-ms-user-select:none;-moz-user-select:none;-moz-box-sizing:border-box;box-sizing:border-box}.noUi-target{position:relative;direction:ltr}.noUi-base{width:100%;height:100%;position:relative}.noUi-origin{position:absolute;right:0;top:0;left:0;bottom:0}.noUi-handle{position:relative;z-index:1}.noUi-stacking .noUi-handle{z-index:10}.noUi-state-tap .noUi-origin{-webkit-transition:left .3s,top .3s;transition:left .3s,top .3s}.noUi-state-drag *{cursor:inherit!important}.noUi-base{-webkit-transform:translate3d(0,0,0);transform:translate3d(0,0,0)}.noUi-horizontal{height:10px}.noUi-horizontal .noUi-handle{width:24px;height:18px;left:-12px;top:-6px}.noUi-vertical{width:10px}.noUi-vertical .noUi-handle{width:18px;height:24px;left:-5px;top:-12px}.noUi-background{background:#FAFAFA;box-shadow:inset 0 1px 1px #f0f0f0}.noUi-connect{background:#3FB8AF;box-shadow:inset 0 0 3px rgba(51,51,51,.45);-webkit-transition:background 450ms;transition:background 450ms}.noUi-origin{border-radius:2px}.noUi-target{border-radius:4px;border:1px solid #D3D3D3;box-shadow:inset 0 1px 1px #F0F0F0,0 3px 6px -5px #BBB}.noUi-target.noUi-connect{box-shadow:inset 0 0 3px rgba(51,51,51,.45),0 3px 6px -5px #BBB}.noUi-dragable{cursor:w-resize}.noUi-vertical .noUi-base{height:135px;}.noUi-vertical .noUi-dragable{cursor:n-resize}.noUi-handle{border:1px solid #D9D9D9;border-radius:3px;background:#FFF;cursor:default;box-shadow:inset 0 0 1px #FFF,inset 0 1px 7px #EBEBEB,0 3px 6px -3px #BBB}.noUi-active{box-shadow:inset 0 0 1px #FFF,inset 0 1px 7px #DDD,0 3px 6px -3px #BBB}.noUi-handle:after,.noUi-handle:before{content:"";display:block;position:absolute;height:9px;width:1px;background:#E8E7E6;left:9px;top:3.5px}.noUi-handle:after{left:12px}.noUi-vertical .noUi-handle:after,.noUi-vertical .noUi-handle:before{width:9px;height:1px;left:3.5px;top:9px}.noUi-vertical .noUi-handle:after{top:12px}[disabled] .noUi-connect,[disabled].noUi-connect{background:#B8B8B8}[disabled] .noUi-handle{cursor:not-allowed} 5 | -------------------------------------------------------------------------------- /index_files/crosstalk-1.2.1/scss/crosstalk.scss: -------------------------------------------------------------------------------- 1 | /* Adjust margins outwards, so column contents line up with the edges of the 2 | parent of container-fluid. */ 3 | .container-fluid.crosstalk-bscols { 4 | margin-left: -30px; 5 | margin-right: -30px; 6 | white-space: normal; 7 | } 8 | 9 | /* But don't adjust the margins outwards if we're directly under the body, 10 | i.e. we were the top-level of something at the console. */ 11 | body > .container-fluid.crosstalk-bscols { 12 | margin-left: auto; 13 | margin-right: auto; 14 | } 15 | 16 | .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { 17 | display: inline-block; 18 | padding-right: 12px; 19 | vertical-align: top; 20 | } 21 | 22 | @media only screen and (max-width:480px) { 23 | .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { 24 | display: block; 25 | padding-right: inherit; 26 | } 27 | } 28 | 29 | /* Relevant BS3 styles to make filter_checkbox() look reasonable without Bootstrap */ 30 | .crosstalk-input { 31 | margin-bottom: 15px; /* a la .form-group */ 32 | .control-label { 33 | margin-bottom: 0; 34 | vertical-align: middle; 35 | } 36 | input[type="checkbox"] { 37 | margin: 4px 0 0; 38 | margin-top: 1px; 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"nav-pills" : "nav-tabs"; 59 | 60 | // determine the heading level of the tabset and tabs 61 | var match = tabset.attr('class').match(/level(\d) /); 62 | if (match === null) 63 | return; 64 | var tabsetLevel = Number(match[1]); 65 | var tabLevel = tabsetLevel + 1; 66 | 67 | // find all subheadings immediately below 68 | var tabs = tabset.find("div.section.level" + tabLevel); 69 | if (!tabs.length) 70 | return; 71 | 72 | // create tablist and tab-content elements 73 | var tabList = $('
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    '); 76 | $(tabs[0]).before(tabContent); 77 | 78 | // build the tabset 79 | var activeTab = 0; 80 | tabs.each(function(i) { 81 | 82 | // get the tab div 83 | var tab = $(tabs[i]); 84 | 85 | // get the id then sanitize it for use with bootstrap tabs 86 | var id = tab.attr('id'); 87 | 88 | // see if this is marked as the active tab 89 | if (tab.hasClass('active')) 90 | activeTab = i; 91 | 92 | // remove any table of contents entries associated with 93 | // this ID (since we'll be removing the heading element) 94 | $("div#" + tocID + " li a[href='#" + id + "']").parent().remove(); 95 | 96 | // sanitize the id for use with bootstrap tabs 97 | id = id.replace(/[.\/?&!#<>]/g, '').replace(/\s/g, '_'); 98 | tab.attr('id', id); 99 | 100 | // get the heading element within it, grab it's text, then remove it 101 | var heading = tab.find('h' + tabLevel + ':first'); 102 | var headingText = heading.html(); 103 | heading.remove(); 104 | 105 | // build and append the tab list item 106 | var a = $('' + headingText + ''); 107 | a.attr('href', '#' + id); 108 | a.attr('aria-controls', id); 109 | var li = $('
  • '); 110 | li.append(a); 111 | tabList.append(li); 112 | 113 | // set it's attributes 114 | tab.attr('role', 'tabpanel'); 115 | tab.addClass('tab-pane'); 116 | tab.addClass('tabbed-pane'); 117 | if (fade) 118 | tab.addClass('fade'); 119 | 120 | // move it into the tab content div 121 | tab.detach().appendTo(tabContent); 122 | }); 123 | 124 | // set active tab 125 | $(tabList.children('li')[activeTab]).addClass('active'); 126 | var active = $(tabContent.children('div.section')[activeTab]); 127 | active.addClass('active'); 128 | if (fade) 129 | active.addClass('in'); 130 | 131 | if (tabset.hasClass("tabset-sticky")) 132 | tabset.rmarkdownStickyTabs(); 133 | } 134 | 135 | // convert section divs with the .tabset class to tabsets 136 | var tabsets = $("div.section.tabset"); 137 | tabsets.each(function(i) { 138 | buildTabset($(tabsets[i])); 139 | }); 140 | }; 141 | 142 | -------------------------------------------------------------------------------- /index.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Genes4Epilepsy" 3 | subtitle: "A curated list of monogenic epilepsy genes" 4 | output: 5 | html_document: 6 | theme: cerulean 7 | self_contained: false 8 | --- 9 | 10 | 11 | ```{r setup, include=FALSE} 12 | knitr::opts_chunk$set(echo = FALSE, 13 | message = FALSE, 14 | warning = FALSE) 15 | library(tidyverse) 16 | library(DT) 17 | ``` 18 | 19 | ```{r} 20 | # Assumptions 21 | # 1) List TSV files named with format EpilepsyGenes_vYYYY-MM.tsv 22 | # 2) List TSV files have columns "HGNC_ID", "Gene", "Ensemble_ID", "Entrez_ID", "OMIM_ID", "Inheritance", "Phenotype(s)" 23 | 24 | # Usage 25 | # 1) Add new version of gene list 26 | # 2) "rm -r index_files" 27 | # 3) knit index.Rmd in Rstudio and check result 28 | # 4) "git add index.Rmd index.html index_files EpilepsyGenes_v*" 29 | # 5) "git commit -m 'updated to version '" 30 | # 6) "git push origin main" 31 | ``` 32 | 33 | ```{r functions} 34 | 35 | ensembl_url <- function(id) { 36 | str_c('', id, '') 38 | } 39 | entrez_url <- function(id) { 40 | str_c('', id, '') 42 | } 43 | omim_url <- function(id) { 44 | str_c('', id, '') 46 | } 47 | hgnc_url <- function(id) { 48 | str_c('', id, '') 50 | } 51 | 52 | 53 | add_urls <- function(data) { 54 | mutate( 55 | data, 56 | HGNC_ID = hgnc_url(HGNC_ID), 57 | Ensemble_ID = ensembl_url(Ensemble_ID), 58 | Entrez_ID = entrez_url(Entrez_ID), 59 | OMIM_ID = omim_url(OMIM_ID) 60 | ) 61 | } 62 | 63 | my_datatable <- function(data, filename) { 64 | datatable( 65 | data, 66 | rownames = FALSE, 67 | escape = FALSE, 68 | filter = 'top', 69 | extensions = 'Buttons', 70 | options = list( 71 | autoWidth=TRUE, 72 | columnDefs = list(list(width = '100px', targets = c('Gene'))), 73 | dom = 'rtipB', 74 | buttons = list( 75 | list(extend = 'csv', filename=filename), 76 | list(extend = 'excel', filename=filename, title='') 77 | ), 78 | initComplete = htmlwidgets::JS( 79 | "function(settings, json) {", 80 | "$('body').css({'font-family': 'Helvetica'});", 81 | "}" 82 | ))) 83 | } 84 | ``` 85 | 86 | 87 | ```{r read_lists} 88 | all_lists <- 89 | tibble( 90 | filename = list.files('.', pattern = 'EpilepsyGenes_v.*.tsv', full.names = T), 91 | version = str_extract(filename, 'v\\d{4}-\\d{2}(?=.tsv)')) %>% 92 | filter(!is.na(version)) %>% 93 | arrange(desc(version)) %>% 94 | mutate(data = map(filename, 95 | read_tsv, 96 | col_types = cols( 97 | HGNC_ID = col_character(), 98 | Gene = col_character(), 99 | Ensemble_ID = col_character(), 100 | Entrez_ID = col_integer(), 101 | OMIM_ID = col_integer(), 102 | Inheritance = col_character(), 103 | `Phenotype(s)` = col_character()), 104 | col_select = c( 105 | Gene, 106 | HGNC_ID, 107 | Ensemble_ID, 108 | Entrez_ID, 109 | OMIM_ID, 110 | Inheritance, 111 | `Phenotype(s)`), 112 | ), 113 | length = map_int(data, nrow)) 114 | 115 | curr_ver <- all_lists$version[1] 116 | ``` 117 | ## `r curr_ver` 118 | 119 | ```{r datatables, results='asis', eval=FALSE} 120 | 121 | all_lists %>% 122 | filter(version == curr_ver) %>% 123 | select(data) %>% 124 | unnest(data) %>% 125 | add_urls() %>% 126 | arrange(Gene) %>% 127 | my_datatable(str_c('Genes4Epilepsy_', curr_ver)) 128 | 129 | ``` 130 | 131 | 132 | ```{r datatables_panelapp, results='asis'} 133 | if (!require(cavalier)) { 134 | stop(str_c('Cavalier not installed - install with "devtools::install_github(\'jemunro/cavalier@dev\')"')) 135 | } 136 | # get the latest PanelApp panels 137 | panel_app <- 138 | bind_rows( 139 | cavalier::get_panelapp_panels('PAA'), 140 | cavalier::get_panelapp_panels('PAE')) %>% 141 | select(id, version) %>% 142 | filter(id %in% c('PAA:202', 'PAE:402')) %>% 143 | pmap_df(function(id, version) { 144 | cavalier::get_panelapp_panel(id, version = version) 145 | }) %>% 146 | mutate( 147 | text = if_else(list_id == 'PAA:202', 148 | 'AU:202', 149 | 'UK:402'), 150 | url = str_c( 151 | '', 157 | text, '')) %>% 158 | select(HGNC_ID = hgnc_id, 159 | PanelApp = url) %>% 160 | chop(PanelApp) %>% 161 | mutate(PanelApp = map_chr(PanelApp, str_c, collapse = ' ')) 162 | 163 | all_lists %>% 164 | filter(version == curr_ver) %>% 165 | select(data) %>% 166 | unnest(data) %>% 167 | left_join(panel_app, by = 'HGNC_ID') %>% 168 | add_urls() %>% 169 | arrange(Gene) %>% 170 | my_datatable(str_c('Genes4Epilepsy_', curr_ver)) 171 | ``` 172 | 173 | 174 | ## Changelog 175 | ```{r changelog} 176 | 177 | all_lists %>% 178 | select(new_ver = version, 179 | new_data = data) %>% 180 | mutate(old_ver = lead(new_ver), 181 | old_data = lead(new_data)) %>% 182 | na.omit() %>% 183 | mutate(changes = map2(new_data, old_data, function(new_data, old_data) { 184 | 185 | added <- 186 | new_data %>% 187 | anti_join(old_data, by = 'HGNC_ID') %>% 188 | mutate(change = 'ADDED') 189 | 190 | removed <- 191 | old_data %>% 192 | anti_join(new_data, by = 'HGNC_ID') %>% 193 | mutate(change = 'REMOVED') 194 | 195 | updated <- 196 | new_data %>% 197 | anti_join(old_data, 198 | by = c("HGNC_ID", 199 | "Gene", 200 | "Ensemble_ID", 201 | "Entrez_ID", 202 | "OMIM_ID", 203 | "Inheritance", 204 | "Phenotype(s)")) %>% 205 | anti_join(added, 206 | by = "HGNC_ID") %>% 207 | mutate(change = 'UPDATED') 208 | 209 | bind_rows( 210 | added, 211 | updated, 212 | removed) 213 | 214 | })) %>% 215 | select(version = new_ver, changes) %>% 216 | unnest(changes) %>% 217 | select(version, change, everything()) %>% 218 | mutate(change = as.factor(change)) %>% 219 | add_urls() %>% 220 | my_datatable(str_c('Genes4Epilepsy_Changelog_v', curr_ver)) 221 | 222 | ``` 223 | 224 | ## All Versions TSV download 225 | ```{r past_versions} 226 | all_lists %>% 227 | select(version, download = filename, length) %>% 228 | mutate(download = 229 | basename(download) %>% 230 | (function(x) 231 | str_c('', x, '') 232 | )) %>% 233 | datatable( 234 | escape = FALSE, 235 | rownames = FALSE, 236 | options = list( 237 | dom = 'rtipB', 238 | initComplete = htmlwidgets::JS( 239 | "function(settings, json) {", 240 | "$('body').css({'font-family': 'Helvetica'});", 241 | "}" 242 | ))) 243 | 244 | ``` 245 | 246 | ## Cite 247 | If you use this Genes4Epilepsy resource, please acknowledge by citing: 248 | [Oliver KL, Scheffer IE, Bennett MF, Grinton BE, Bahlo M, Berkovic SF. Genes4Epilepsy: An epilepsy gene resource. Epilepsia. 2023 May;64(5):1368-1375. doi: 10.1111/epi.17547](https://onlinelibrary.wiley.com/doi/10.1111/epi.17547) 249 | 250 | This webpage developed by [Jacob E. 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You may obtain a copy of the License at: 7 | * http://www.apache.org/licenses/LICENSE-2.0 8 | * 9 | * Unless required by applicable law or agreed to in writing, software distributed under 10 | * the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF 11 | * ANY KIND, either express or implied. See the License for the specific language 12 | * governing permissions and limitations under the License. 13 | * 14 | * @author Brian Reavis 15 | */ 16 | .selectize-control.plugin-drag_drop.multi > .selectize-input > div.ui-sortable-placeholder { 17 | visibility: visible !important; 18 | background: #f2f2f2 !important; 19 | background: rgba(0, 0, 0, 0.06) !important; 20 | border: 0 none !important; 21 | -webkit-box-shadow: inset 0 0 12px 4px #ffffff; 22 | box-shadow: inset 0 0 12px 4px #ffffff; 23 | } 24 | .selectize-control.plugin-drag_drop .ui-sortable-placeholder::after { 25 | content: '!'; 26 | visibility: hidden; 27 | } 28 | .selectize-control.plugin-drag_drop .ui-sortable-helper { 29 | -webkit-box-shadow: 0 2px 5px rgba(0, 0, 0, 0.2); 30 | box-shadow: 0 2px 5px rgba(0, 0, 0, 0.2); 31 | } 32 | .selectize-dropdown-header { 33 | position: relative; 34 | padding: 3px 12px; 35 | border-bottom: 1px solid #d0d0d0; 36 | background: #f8f8f8; 37 | -webkit-border-radius: 4px 4px 0 0; 38 | 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relative; 73 | padding-right: 24px !important; 74 | } 75 | .selectize-control.plugin-remove_button [data-value] .remove { 76 | z-index: 1; 77 | /* fixes ie bug (see #392) */ 78 | position: absolute; 79 | top: 0; 80 | right: 0; 81 | bottom: 0; 82 | width: 17px; 83 | text-align: center; 84 | font-weight: bold; 85 | font-size: 12px; 86 | color: inherit; 87 | text-decoration: none; 88 | vertical-align: middle; 89 | display: inline-block; 90 | padding: 1px 0 0 0; 91 | border-left: 1px solid rgba(0, 0, 0, 0); 92 | -webkit-border-radius: 0 2px 2px 0; 93 | -moz-border-radius: 0 2px 2px 0; 94 | border-radius: 0 2px 2px 0; 95 | -webkit-box-sizing: border-box; 96 | -moz-box-sizing: border-box; 97 | box-sizing: border-box; 98 | } 99 | .selectize-control.plugin-remove_button [data-value] .remove:hover { 100 | background: rgba(0, 0, 0, 0.05); 101 | } 102 | .selectize-control.plugin-remove_button [data-value].active .remove { 103 | border-left-color: rgba(0, 0, 0, 0); 104 | } 105 | 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cursor: pointer; 174 | margin: 0 3px 3px 0; 175 | padding: 1px 3px; 176 | background: #efefef; 177 | color: #333333; 178 | border: 0 solid rgba(0, 0, 0, 0); 179 | } 180 | .selectize-control.multi .selectize-input > div.active { 181 | background: #428bca; 182 | color: #ffffff; 183 | border: 0 solid rgba(0, 0, 0, 0); 184 | } 185 | .selectize-control.multi .selectize-input.disabled > div, 186 | .selectize-control.multi .selectize-input.disabled > div.active { 187 | color: #808080; 188 | background: #ffffff; 189 | border: 0 solid rgba(77, 77, 77, 0); 190 | } 191 | .selectize-input > input { 192 | display: inline-block !important; 193 | padding: 0 !important; 194 | min-height: 0 !important; 195 | max-height: none !important; 196 | max-width: 100% !important; 197 | margin: 0 !important; 198 | text-indent: 0 !important; 199 | border: 0 none !important; 200 | background: none !important; 201 | line-height: inherit !important; 202 | -webkit-user-select: auto !important; 203 | -webkit-box-shadow: none !important; 204 | box-shadow: none !important; 205 | } 206 | .selectize-input > input::-ms-clear { 207 | display: none; 208 | } 209 | .selectize-input > input:focus { 210 | outline: none !important; 211 | } 212 | .selectize-input::after { 213 | content: ' '; 214 | display: block; 215 | clear: left; 216 | } 217 | .selectize-input.dropdown-active::before { 218 | content: ' '; 219 | display: block; 220 | position: absolute; 221 | background: #ffffff; 222 | height: 1px; 223 | bottom: 0; 224 | left: 0; 225 | right: 0; 226 | } 227 | .selectize-dropdown { 228 | position: absolute; 229 | z-index: 10; 230 | border: 1px solid #d0d0d0; 231 | background: #ffffff; 232 | margin: -1px 0 0 0; 233 | border-top: 0 none; 234 | -webkit-box-sizing: border-box; 235 | -moz-box-sizing: border-box; 236 | box-sizing: border-box; 237 | -webkit-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1); 238 | box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1); 239 | -webkit-border-radius: 0 0 4px 4px; 240 | -moz-border-radius: 0 0 4px 4px; 241 | border-radius: 0 0 4px 4px; 242 | } 243 | .selectize-dropdown [data-selectable] { 244 | cursor: pointer; 245 | overflow: hidden; 246 | } 247 | .selectize-dropdown [data-selectable] .highlight { 248 | background: rgba(255, 237, 40, 0.4); 249 | -webkit-border-radius: 1px; 250 | -moz-border-radius: 1px; 251 | border-radius: 1px; 252 | } 253 | .selectize-dropdown [data-selectable], 254 | .selectize-dropdown .optgroup-header { 255 | padding: 3px 12px; 256 | } 257 | .selectize-dropdown .optgroup:first-child .optgroup-header { 258 | border-top: 0 none; 259 | } 260 | .selectize-dropdown .optgroup-header { 261 | color: #777777; 262 | background: #ffffff; 263 | cursor: default; 264 | } 265 | .selectize-dropdown .active { 266 | background-color: #f5f5f5; 267 | color: #262626; 268 | } 269 | .selectize-dropdown .active.create { 270 | color: #262626; 271 | } 272 | .selectize-dropdown .create { 273 | color: rgba(51, 51, 51, 0.5); 274 | } 275 | .selectize-dropdown-content { 276 | overflow-y: auto; 277 | overflow-x: hidden; 278 | max-height: 200px; 279 | } 280 | .selectize-control.single .selectize-input, 281 | .selectize-control.single .selectize-input input { 282 | cursor: pointer; 283 | } 284 | .selectize-control.single .selectize-input.input-active, 285 | .selectize-control.single .selectize-input.input-active input { 286 | cursor: text; 287 | } 288 | .selectize-control.single .selectize-input:after { 289 | content: ' '; 290 | display: block; 291 | position: absolute; 292 | top: 50%; 293 | right: 17px; 294 | margin-top: -3px; 295 | width: 0; 296 | height: 0; 297 | border-style: solid; 298 | border-width: 5px 5px 0 5px; 299 | border-color: #333333 transparent transparent transparent; 300 | } 301 | .selectize-control.single .selectize-input.dropdown-active:after { 302 | margin-top: -4px; 303 | border-width: 0 5px 5px 5px; 304 | border-color: transparent transparent #333333 transparent; 305 | } 306 | .selectize-control.rtl.single .selectize-input:after { 307 | left: 17px; 308 | right: auto; 309 | } 310 | .selectize-control.rtl .selectize-input > input { 311 | margin: 0 4px 0 -2px !important; 312 | } 313 | .selectize-control .selectize-input.disabled { 314 | opacity: 0.5; 315 | background-color: #ffffff; 316 | } 317 | .selectize-dropdown, 318 | .selectize-dropdown.form-control { 319 | height: auto; 320 | padding: 0; 321 | margin: 2px 0 0 0; 322 | z-index: 1000; 323 | background: #ffffff; 324 | border: 1px solid #cccccc; 325 | border: 1px solid rgba(0, 0, 0, 0.15); 326 | -webkit-border-radius: 4px; 327 | -moz-border-radius: 4px; 328 | border-radius: 4px; 329 | -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175); 330 | box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175); 331 | } 332 | .selectize-dropdown .optgroup-header { 333 | font-size: 12px; 334 | line-height: 1.42857143; 335 | } 336 | .selectize-dropdown .optgroup:first-child:before { 337 | display: none; 338 | } 339 | .selectize-dropdown .optgroup:before { 340 | content: ' '; 341 | display: block; 342 | height: 1px; 343 | margin: 9px 0; 344 | overflow: hidden; 345 | background-color: #e5e5e5; 346 | margin-left: -12px; 347 | margin-right: -12px; 348 | } 349 | .selectize-dropdown-content { 350 | padding: 5px 0; 351 | } 352 | .selectize-dropdown-header { 353 | padding: 6px 12px; 354 | } 355 | .selectize-input { 356 | min-height: 34px; 357 | } 358 | .selectize-input.dropdown-active { 359 | -webkit-border-radius: 4px; 360 | -moz-border-radius: 4px; 361 | border-radius: 4px; 362 | } 363 | .selectize-input.dropdown-active::before { 364 | display: none; 365 | } 366 | .selectize-input.focus { 367 | border-color: #66afe9; 368 | outline: 0; 369 | -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6); 370 | box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6); 371 | } 372 | .has-error .selectize-input { 373 | border-color: #a94442; 374 | -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); 375 | box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); 376 | } 377 | .has-error .selectize-input:focus { 378 | border-color: #843534; 379 | -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483; 380 | box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483; 381 | } 382 | .selectize-control.multi .selectize-input.has-items { 383 | padding-left: 9px; 384 | padding-right: 9px; 385 | } 386 | .selectize-control.multi .selectize-input > div { 387 | -webkit-border-radius: 3px; 388 | -moz-border-radius: 3px; 389 | border-radius: 3px; 390 | } 391 | .form-control.selectize-control { 392 | padding: 0; 393 | height: auto; 394 | border: none; 395 | background: none; 396 | -webkit-box-shadow: none; 397 | box-shadow: none; 398 | -webkit-border-radius: 0; 399 | -moz-border-radius: 0; 400 | border-radius: 0; 401 | } 402 | -------------------------------------------------------------------------------- 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