{"id":54283,"date":"2024-06-16T13:50:49","date_gmt":"2024-06-16T05:50:49","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54283"},"modified":"2024-06-16T13:50:49","modified_gmt":"2024-06-16T05:50:49","slug":"%e8%b6%85%e7%ba%a7%e4%be%a6%e6%8e%a2singler%ef%bc%8c%e6%8f%ad%e9%9c%b2%e5%8d%95%e7%bb%86%e8%83%9e%e6%95%b0%e6%8d%ae%e7%bb%86%e8%83%9e%e7%b1%bb%e5%9e%8b%e7%9a%84%e5%a5%a5%e7%a7%98","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54283","title":{"rendered":"\u8d85\u7ea7\u4fa6\u63a2SingleR\uff0c\u63ed\u9732\u5355\u7ec6\u80de\u6570\u636e\u7ec6\u80de\u7c7b\u578b\u7684\u5965\u79d8"},"content":{"rendered":"


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\n<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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#e7e7eb;}@supports(-webkit-overflow-scrolling:touch){.rich_media_title{font-weight:700}}.rich_media_meta{display:inline-block;vertical-align:middle;padding:0 0 10px 0;font-size:15px;-webkit-tap-highlight-color:rgba(0,0,0,0)}.rich_media_meta.icon_appmsg_tag{margin-right:0px}.rich_media_meta.meta_tag_text{margin-right:0}.rich_media_meta_list em{font-style:normal}.rich_media_meta_text{color:#a5a5a5;}p{margin:0;}.msgBox{margin-top:20px;padding-top:20px;padding-left:50px;overflow:hidden;border-top:2px dashed #09a2ff;}.msg{padding-top:7px;clear:both;}.msgBody{float:right;width:100%;margin-left:55px;padding-bottom:15px;border-bottom:1px dashed #e0e0e0;}.userHeadImg{float:left;margin-left:-50px;}.userHeadImg img{width:40px;height:40px;margin-right:10px;border-radius:3px;}.userName{color:#888888;line-height:24px;font-size:14px;margin:5px 0 5px 0;height:24px;}.replyBody,.autherBody{color:#565656;font-size:15px;}.replyIcon{border-left:4px solid 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solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar 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rich_media_meta_text\">\u5c0f\u679c  <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c  <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-11-06 19:01:03<\/em><\/div>\n<p><content><\/p>\n<div class=\"topic\">\n<p>\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<p><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2812010014583390210#wechat_redirect\" title=\"R\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#R\u4ee3\u7801<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><\/p>\n<\/div>\n<p style=\"text-align: center;\" data-mpa-powered-by=\"yiban.io\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2216796875\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"1024\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_snVaia0ia8A5L1rXZ1xVtIEYJhRYwg.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAyOD23lzsibR9jQXL7ibIszDztr50BBOLhoBOyv5vjbFzPuGOYiasnVaia0ia8A5L1rXZ1xVtIEYJhRYwg\/640?wx_fmt=jpeg'\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u55e8\uff0c\u679c\u7c89\u513f\u4eec\uff01\u4eca\u5929\u5c0f\u679c\u8981\u548c\u5927\u5bb6\u4e00\u8d77\u63a2\u7d22\u7684\u662f\u5355\u7ec6\u80de\u6570\u636e\u7684\u4e16\u754c\uff0c\u51c6\u786e\u7684\u8bf4\uff0c\u6211\u4eec\u8981\u548c\u4e00\u4e2a\u8d85\u7ea7\u4fa6\u63a2SingleR\u4e00\u8d77\u63ed\u9732\u8fd9\u4e9b\u7ec6\u80de\u7684\u5965\u79d8\u3002\u5982\u679c\u4f60\u66fe\u7ecf\u82e6\u607c\u4e8e\u5982\u4f55\u7ed9\u5355\u7ec6\u80de\u6570\u636e\u6253\u4e0a\u6b63\u786e\u7684\u6807\u7b7e\uff0c\u800c\u975e\u4e00\u5806\u65e0\u610f\u4e49\u7684\u6570\u5b57\uff1b\u6216\u8005\u4f60\u4e5f\u5c1d\u8bd5\u8fc7\u5404\u79cd\u5404\u6837\u7684\u7ec6\u80de\u6ce8\u91ca\u65b9\u6cd5\uff0c\u5374\u53d1\u73b0\u5b83\u4eec\u8981\u4e48\u592a\u590d\u6742\uff0c\u8981\u4e48\u592a\u4e3b\u89c2\uff0c\u65e0\u6cd5\u6ee1\u8db3\u4f60\u7684\u9700\u6c42\u3002\u90a3\u4e48\u4eca\u5929\u7684\u5185\u5bb9\u4e00\u5b9a\u80fd\u5e2e\u5230\u4f60\uff0c\u8ddf\u4e0a\u5c0f\u679c\u7684\u6b65\u4f10\uff0c\u6211\u4eec\u51fa\u53d1\u5566\u3002<\/span><br \/><\/p>\n<p><strong><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.49186046511627907\" data-type=\"png\" data-w=\"860\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_UEFx0NKJyZTDia6BO1W3fZsNddgNFw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHfzzzia2ujREtg2k5jDEGRmWNNibUEFx0NKJyZTDia6BO1W3fZsNddgNFw\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><span style=\"color: rgb(2, 30, 170);\">SingleR\u7684\u524d\u4e16\u4eca\u751f<\/span><\/strong><\/p>\n<p><span style=\"font-size: 14px;\">SingleR\u662f\u4e00\u4e2a\u7528\u4e8e\u5bf9\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u7ec6\u80de\u7c7b\u578b\u81ea\u52a8\u6ce8\u91ca\u7684R\u5305\uff0c\u5b83\u4e8e2019\u5e74\u7531Aran\u7b49\u4eba\u53d1\u8868\u5728Nature Immunology\u4e0a\uff08<\/span><span style=\"font-size: 14px;\">https:\/\/www.nature.com\/articles\/s41590-018-0276-y<\/span><span style=\"font-size: 14px;\"> \uff09\u3002SingleR\u7684\u5f00\u53d1\u6e90\u4e8e\u4f5c\u8005\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u6ce8\u91ca\u65b9\u6cd5\u7684\u4e0d\u6ee1\u3002\u4f5c\u8005\u8ba4\u4e3a\uff0c\u76ee\u524d\u7684\u5355\u7ec6\u80de\u6570\u636e\u6ce8\u91ca\u65b9\u6cd5\u5927\u591a\u4f9d\u8d56\u4e8e\u4eba\u5de5\u9009\u62e9\u7684marker\u57fa\u56e0\u6216\u8005\u57fa\u4e8e\u805a\u7c7b\u7684\u5047\u8bbe\uff0c\u8fd9\u4e9b\u65b9\u6cd5\u90fd\u5b58\u5728\u4e00\u5b9a\u7684\u504f\u5dee\u548c\u5c40\u9650\u6027\u3002\u56e0\u6b64\uff0c\u4f5c\u8005\u63d0\u51fa\u4e86\u8fd9\u4e2a\u57fa\u4e8e\u53c2\u8003\u6570\u636e\u96c6\u7684\u65e0\u504f\u5dee\u7684\u5355\u7ec6\u80de\u6570\u636e\u6ce8\u91ca\u65b9\u6cd5\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">SingleR\u7684\u6838\u5fc3\u601d\u60f3\u662f\u5229\u7528\u5df2\u77e5\u7ec6\u80de\u7c7b\u578b\u7684\u53c2\u8003\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6\uff0c\u901a\u8fc7\u8ba1\u7b97\u6bcf\u4e2a\u5355\u7ec6\u80de\u4e0e\u53c2\u8003\u7ec6\u80de\u4e4b\u95f4\u7684\u76f8\u4f3c\u5ea6\uff0c\u6765\u63a8\u65ad\u6bcf\u4e2a\u5355\u7ec6\u80de\u7684\u6700\u4f73\u5339\u914d\u7ec6\u80de\u7c7b\u578b\u3002SingleR\u4e0d\u9700\u8981\u7528\u6237\u63d0\u4f9b\u4efb\u4f55\u5148\u9a8c\u4fe1\u606f\u6216\u53c2\u6570\uff0c\u4e5f\u4e0d\u9700\u8981\u7528\u6237\u8fdb\u884c\u4efb\u4f55\u805a\u7c7b\u6216\u964d\u7ef4\u64cd\u4f5c\uff0c\u53ea\u9700\u8981\u8f93\u5165\u5355\u7ec6\u80de\u6570\u636e\u548c\u53c2\u8003\u6570\u636e\u96c6\uff0c\u5c31\u53ef\u4ee5\u5f97\u5230\u6bcf\u4e2a\u5355\u7ec6\u80de\u7684\u7ec6\u80de\u7c7b\u578b\u6807\u7b7e\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">Sounds amazing? \u90a3\u4e48\u5982\u4f55\u4f7f\u7528SingleR\u5462\uff1f\u5176\u5b9e\u5f88\u7b80\u5355\uff0c\u53ea\u9700\u8981\u4e09\u6b65\uff1a<\/span><\/p>\n<p><span style=\"color: rgb(2, 30, 170);\"><strong>\u7b2c\u4e00\u6b65\uff1a\u5b89\u88c5\u548c\u52a0\u8f7dSingleR\u5305<\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4eceBioconductor\u5b89\u88c5<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span> (!requireNamespace(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>, quietly = <span class=\"code-snippet__keyword\">TRUE<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"SingleR\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u52a0\u8f7d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(SingleR)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"color: rgb(2, 30, 170);\"><strong>\u7b2c\u4e8c\u6b65\uff1a\u51c6\u5907\u8f93\u5165\u6570\u636e<\/strong><\/span><\/p>\n<p><span style=\"font-size: 15px;\">SingleR\u9700\u8981\u4e24\u4e2a\u8f93\u5165\u6570\u636e\uff1a\u4e00\u662f\u6211\u4eec\u8981\u6ce8\u91ca\u7684\u5355\u7ec6\u80de\u6570\u636e\uff08\u79f0\u4e3atest data\uff09\uff0c\u53e6\u4e00\u4e2a\u662f\u4f60\u8981\u7528\u6765\u5339\u914d\u7684\u53c2\u8003\u6570\u636e\u96c6\uff08\u79f0\u4e3areference data\uff09\u3002test data\u5e94\u8be5\u662f\u4e00\u4e2a\u5305\u542b\u4e86\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u77e9\u9635\u6216\u5bf9\u8c61\uff0c\u5176\u4e2d\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u57fa\u56e0\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u7ec6\u80de\u3002reference data\u5e94\u8be5\u662f\u4e00\u4e2a\u5305\u542b\u4e86\u7eaf\u7ec6\u80de\u7c7b\u578b\u8f6c\u5f55\u7ec4\u6570\u636e\u548c\u5bf9\u5e94\u6807\u7b7e\u7684\u77e9\u9635\u6216\u5bf9\u8c61\uff0c\u5176\u4e2d\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u57fa\u56e0\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u53c2\u8003\u7ec6\u80de\u3002<\/span><\/p>\n<p><span style=\"font-size: 15px;\">##\u8f93\u5165\u7684\u53c2\u8003\u6570\u636e\u96c6<\/span><\/p>\n<p><span style=\"font-size: 15px;\">\u5982\u679c\u4f60\u6ca1\u6709\u81ea\u5df1\u7684\u53c2\u8003\u6570\u636e\u96c6\uff0c\u4e0d\u7528\u62c5\u5fc3\uff0cSingleR\u63d0\u4f9b\u4e867\u4e2a\u5185\u7f6e\u7684\u53c2\u8003\u6570\u636e\u96c6\u4f9b\u4f60\u9009\u62e9\u3002\u76ee\u524d\u6709\u4ee5\u4e0b\u51e0\u4e2a\u9009\u9879\uff1a<\/span><\/p>\n<p><span style=\"font-size: 15px;\">Human Primary Cell Atlas (HPCA)\uff1a\u5305\u542b\u4e8632\u79cd\u4eba\u7c7b\u4e3b\u8981\u7ec6\u80de\u7c7b\u578b\u7684\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6\uff0c\u6765\u6e90\u4e8eImmunological Genome Project (ImmGen)\u548cHuman Cell Atlas (HCA) <\/span><\/p>\n<p><span style=\"font-size: 15px;\">Blueprint Encode Data\uff1a\u5305\u542b\u4e86713\u79cd\u4eba\u7c7b\u9020\u8840\u7ec6\u80de\u7c7b\u578b\u7684\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6\uff0c\u6765\u6e90\u4e8eBlueprint\u548cENCODE\u9879\u76ee <\/span><\/p>\n<p><span style=\"font-size: 15px;\">Monaco Immune Data\uff1a\u5305\u542b\u4e8628\u79cd\u4eba\u7c7b\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6\uff0c\u6765\u6e90\u4e8eMonaco\u7b49\u4eba\u7684\u7814\u7a76 <\/span><\/p>\n<p><span style=\"font-size: 15px;\">Novershtern Hematopoietic Data\uff1a\u5305\u542b\u4e8638\u79cd\u4eba\u7c7b\u9020\u8840\u7ec6\u80de\u7c7b\u578b\u7684\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6\uff0c\u6765\u6e90\u4e8eNovershtern\u7b49\u4eba\u7684\u7814\u7a76 <\/span><\/p>\n<p><span style=\"font-size: 15px;\">Mouse RNAseq Data\uff1a\u5305\u542b\u4e8638\u79cd\u5c0f\u9f20\u7ec6\u80de\u7c7b\u578b\u7684\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6\uff0c\u6765\u6e90\u4e8eImmGen\u9879\u76ee <\/span><\/p>\n<p><span style=\"font-size: 15px;\">\u4f60\u53ef\u4ee5\u6839\u636e\u4f60\u7684\u6570\u636e\u7684\u7269\u79cd\u548c\u7ec6\u80de\u7c7b\u578b\u6765\u9009\u62e9\u5408\u9002\u7684\u53c2\u8003\u6570\u636e\u96c6\u3002\u8fd9\u91cc\u6211\u4eec\u9009\u7528\u7684\u662f\u4eba\u7c7b\u80be\u810f\u6570\u636e\uff0c\u6240\u4ee5\u9009\u62e9Human Primary Cell Atlas\u4f5c\u4e3a\u53c2\u8003\u6570\u636e\u96c6<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\">#\u53ef\u4ee5\u7528celldex\u5305\u7684\u5185\u7f6e\u51fd\u6570\u76f4\u63a5\u52a0\u8f7d\u53c2\u8003\u6570\u636e\u96c6\uff1a<\/span><\/code><code><span class=\"code-snippet_outer\">ref.hpca <- HumanPrimaryCellAtlasData()<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6216\u8005\u5bfc\u5165\u4e4b\u524d\u4e0b\u8f7d\u597d\u7684\u53c2\u8003\u6570\u636e\u96c6<\/span><\/code><code><span class=\"code-snippet_outer\">ref.hpca <- get(load(\"hpca.Rdata\"))<\/span><\/code><code><span class=\"code-snippet_outer\">##\u9700\u8981\u6ce8\u91ca\u7684\u5355\u7ec6\u80de\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">\u8fd9\u91cc\u6211\u4eec\u9009\u62e9\u4e86\u4e00\u5957\u5305\u542b4000\u591a\u4e2a\u7ec6\u80de\u7684\u4eba\u7c7b\u80be\u810f\u6837\u672c\u4f5c\u4e3a\u8f93\u5165\u6570\u636e\uff1a<\/span><\/code><code><span class=\"code-snippet_outer\">https:\/\/www.ncbi.nlm.nih.gov\/geo\/download\/?acc=GSM5225906&format=file&file=GSM5225906%5Fs200929N8%2Eexpression%5Fmatrix%2Etxt%2Egz<\/span><\/code><code><span class=\"code-snippet_outer\"># \u5bfc\u5165\u8868\u8fbe\u77e9\u9635\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">data <- read.table(file=\"GSM5225906_s200929N8.expression_matrix.txt.gz\")<\/span><\/code><code><span class=\"code-snippet_outer\"># \u5bfc\u5165\u6240\u9700\u7684\u5e93<\/span><\/code><code><span class=\"code-snippet_outer\">library(Seurat)<\/span><\/code><code><span class=\"code-snippet_outer\">library(SingleR)<\/span><\/code><code><span class=\"code-snippet_outer\">library(celldex)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5e38\u89c4\u7684\u6570\u636e\u9884\u5904\u7406\uff0c\u521b\u5efa\u4e00\u4e2aSeurat\u5bf9\u8c61\uff08scRNA\uff09\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">scRNA <- CreateSeuratObject(counts = data, min.cells = 3,min.features = 200, project = \"kidney\")<\/span><\/code><code><span class=\"code-snippet_outer\">scRNA <- SCTransform(scRNA)<\/span><\/code><code><span class=\"code-snippet_outer\">scRNA <- RunPCA(scRNA, verbose = F)<\/span><\/code><code><span class=\"code-snippet_outer\">scRNA <- RunUMAP(scRNA, dims = 1:15)<\/span><\/code><code><span class=\"code-snippet_outer\">scRNA <- FindNeighbors(scRNA, dims = 1:15) %>% FindClusters(resolution = 0.6)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u4e3a\u8282\u7ea6\u65f6\u95f4\uff0c\u6211\u4eec\u9009\u53d6\u524d500\u4e2a\u7ec6\u80de<\/span><\/code><code><span class=\"code-snippet_outer\">sce <- scRNA[,1:500]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u83b7\u53d6\u6807\u51c6\u5316\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">expdata <- GetAssayData(sce, slot=\"data\")<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"color: rgb(2, 30, 170);\"><strong>\u7b2c\u4e09\u6b65\uff1a\u8fdb\u884csingleR\u6ce8\u91ca<\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\">#\u8fdb\u884c\u6ce8\u91ca\uff0c\u6ce8\u610fSingleR\u81ea\u5e26\u53c2\u8003\u96c6\u7684\u6807\u7b7e\u662f\u5206\u522b\u662fmain,ont\u548cfine\uff0cfine\u548cont\u8868\u793a\u66f4\u7ec6\u5206\u7684\u6807\u7b7e,\u8fd9\u91cc\u6211\u4eec\u7528main\u7684\u7ed3\u679c\u5c31\u53ef\u4ee5\u4e86\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">sce.hpca <- SingleR(test = expdata, ref = ref.hpca, labels = ref.hpca$label.main)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8bbe\u7f6e\u7ec6\u80de\u7c7b\u578b\u7684\u6807\u7b7e<\/span><\/code><code><span class=\"code-snippet_outer\">sce@meta.data$celltype <-sce.hpca$labels<\/span><\/code><code><span class=\"code-snippet_outer\">#\u53ef\u89c6\u5316<\/span><\/code><code><span class=\"code-snippet_outer\">DimPlot(sce, group.by = c(\"seurat_clusters\", \"celltype\"),reduction = \"umap\")<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.4208791208791209\" data-type=\"png\" data-w=\"910\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_UbbaonV5CsAmUqLTZ0jftMjM1stupg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghH6XwT6gZDRbvU0DtcIPVDVg9lUbbaonV5CsAmUqLTZ0jftMjM1stupg\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"font-size: 14px;\">\u5982\u679c\u60f3\u8981\u66f4\u6362\u53c2\u8003\u6570\u636e\u96c6\u53ea\u9700\u4e00\u952e\u5bfc\u5165<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\">ref.be <- BlueprintEncodeData()<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u5e76\u91cd\u590d\u7b2c\u4e09\u6b65\u5373\u53ef<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.4781523096129838\" data-type=\"png\" data-w=\"801\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_wgmUhaj151CkCQsHuZPHu1rLPrSReA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHel2m8jRz4HQRyDbbA1snuYqlwgmUhaj151CkCQsHuZPHu1rLPrSReA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"font-size: 14px;\">\u53ef\u4ee5\u53d1\u73b0\u66f4\u6362\u53c2\u8003\u96c6\u4e4b\u540e\uff0c\u6ce8\u91ca\u7684\u7ec6\u80de\u7c7b\u578b\u53d1\u751f\u4e86\u53d8\u5316\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u5f53\u7136\u8fd9\u53ea\u662f\u6700\u57fa\u7840\u7684\u7ec6\u80de\u6ce8\u91ca\u624b\u6bb5\uff0c\u662f\u5426\u51c6\u786e\u8fd8\u9700\u8981\u8fdb\u4e00\u6b65\u8bc4\u4f30\uff0c\u60f3\u8981\u5b66\u4e60\u66f4\u9ad8\u9636\u7684\u7ec6\u80de\u6ce8\u91ca\uff0c\u8bf7\u6301\u7eed\u5173\u6ce8\u5c0f\u679c\u7684\u540e\u671f\u5206\u4eab\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u4eca\u5929\u7684\u63a2\u7d22\u5c31\u8981\u7ed3\u675f\u4e86\u3002\u5e0c\u671b\u4f60\u5df2\u7ecf\u4e86\u89e3\u4e86\u5982\u4f55\u4f7f\u7528\u8fd9\u4e2a\u8d85\u7ea7\u4fa6\u63a2SingleR\u6765\u63ed\u9732\u4f60\u7684\u5355\u7ec6\u80de\u6570\u636e\u4e2d\u7684\u7ec6\u80de\u7c7b\u578b\u7684\u5965\u79d8\u3002\u5feb\u8bd5\u8bd5\u770b\u5427\uff0c\u4e5f\u53ef\u4ee5\u6210\u4e3a\u4e00\u4e2a\u8d85\u7ea7\u7684\u5355\u7ec6\u80de\u6570\u636e\u79d1\u5b66\u5bb6\uff01<\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;text-align: left;\">\n<section style=\"font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;\">\n<section style=\"display: inline-block;width: 536px;border-width: 0px 0px 0px 10px;border-style: solid;border-left-color: rgb(144, 215, 236);border-right-color: rgb(46, 172, 109);box-shadow: rgb(0, 0, 0) 0px 0px 0px;border-bottom-left-radius: 0px;\">\n<section powered-by=\"xiumi.us\" style=\"padding-right: 3px;padding-left: 3px;\">\n<section style=\"margin-top: 0.95em;margin-bottom: -0.65em;display: inline-block;width: 520px;vertical-align: top;\">\n<section style=\"margin-top: -1em;padding: 3px 10px;display: inline-block;vertical-align: top;background-color: rgb(255, 255, 255);color: rgb(0, 154, 68);\">\n<p><strong>\u5f80\u671f\u63a8\u8350<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;\">\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" textvalue=\"1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4<\/a><br \/><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" 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