{"id":30185,"date":"2024-02-28T18:07:32","date_gmt":"2024-02-28T10:07:32","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30185"},"modified":"2024-02-28T18:07:33","modified_gmt":"2024-02-28T10:07:33","slug":"scran%ef%bc%9a%e7%bb%86%e8%83%9e%e8%a1%a8%e8%be%be%e5%a4%a7%e6%95%b0%e6%8d%ae%e7%9a%84%e6%99%ba%e8%83%bd%e5%a4%84%e7%90%86%e5%b7%a5%e5%85%b7%ef%bc%8c%e5%8a%a9%e4%bd%a0%e6%88%90%e4%b8%ba%e8%a1%a8","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30185","title":{"rendered":"scran\uff1a\u7ec6\u80de\u8868\u8fbe\u5927\u6570\u636e\u7684\u667a\u80fd\u5904\u7406\u5de5\u5177\uff0c\u52a9\u4f60\u6210\u4e3a\u8868\u8fbe\u5206\u6790\u4e13\u5bb6\uff01"},"content":{"rendered":"<p><strong>scran\uff1a\u7ec6\u80de\u8868\u8fbe\u5927\u6570\u636e\u7684\u667a\u80fd\u5904\u7406\u5de5\u5177\uff0c\u52a9\u4f60\u6210\u4e3a\u8868\u8fbe\u5206\u6790\u4e13\u5bb6\uff01<\/strong><\/p>\n<p>\u5728\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u524d\uff0c\u5c0f\u679c\u8981\u548c\u5927\u5bb6\u4e00\u8d77\u6765\u56de\u987e\u4e00\u4e0b\u76ee\u524d\u4e3b\u6d41\u7684scRNA-seq\u5206\u6790\u6b65\u9aa4\uff0c\u5927\u5bb6\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u7684\u6b65\u9aa4\u662f\u5426\u8fdb\u884c\u8fc7\u4e00\u4e9b\u603b\u7ed3\u5462\uff1f\u6ca1\u6709\u4e5f\u6ca1\u5173\u7cfb\uff0c\u63a5\u4e0b\u6765\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u56de\u987e\u4e00\u4e0b\u5427\uff01<\/p>\n<ul>\n<li>\u901a\u8fc7\u4e3b\u6d41\u6570\u636e\u5e93\/\u7b2c\u4e09\u65b9\u5de5\u5177\u7b49\u65b9\u6cd5\u4e0b\u8f7d\u5206\u6790\u6240\u9700\u8981\u7684\u6d4b\u5e8f\u6570\u636e\uff1b<\/li>\n<li>\u9884\u5904\u7406\u6d4b\u5e8f\u6570\u636e\uff0c\u901a\u8fc7\u9884\u5904\u7406\u751f\u6210\u8868\u8fbe\u8ba1\u6570\u77e9\u9635\uff08\u884c\u4e3a\u57fa\u56e0\/\u8f6c\u5f55\u672c\uff0c\u5217\u4e3a\u7ec6\u80de\uff09\uff0c\u540c\u65f6\u521b\u5efa\u5355\u7ec6\u80de\u6d4b\u8bd5\u5bf9\u8c61\uff1b<\/li>\n<li>\u6570\u636e\u8d28\u63a7\uff1b<\/li>\n<li>\u6570\u636e\u6807\u51c6\u5316\uff1b<\/li>\n<li>\u6570\u636e\u7b5b\u9009\u5e76\u5206\u6790\uff1b<\/li>\n<li>\u6570\u636e\u964d\u7ef4\u548c\u964d\u566a\uff1b<\/li>\n<li>\uff08\u770b\u60c5\u51b5\u64cd\u4f5c\uff09\u6574\u5408\u591a\u6279\u6b21\u6570\u636e\u3002<\/li>\n<\/ul>\n<p>\u901a\u8fc7\u5c0f\u679c\u548c\u5927\u5bb6\u7684\u56de\u987e\uff0c\u4f60\u60f3\u8d77\u6765\u4e86\u8fd9\u4e9b\u6d41\u7a0b\u4e86\u561b\uff1f\u56de\u987e\u8fc7\u540e\uff0c\u8fdb\u5165\u4eca\u5929\u7684\u6b63\u9898\uff0c\u6211\u4eec\u4eca\u5929\u8981\u4e00\u8d77\u5b66\u4e60\u7684\u5c31\u662f\u5bf9scRNA-seq\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316\u5904\u7406\u7684\u4e00\u4e2a\u5e38\u7528\u5de5\u5177\u5305\uff1ascran\u3002\u63a5\u4e0b\u6765\u5c31\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770bscran\u662f\u5982\u4f55\u5bf9\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316\u5904\u7406\u7684\u5427\uff01<\/p>\n<p><strong>scran\u7684\u5b89\u88c5<\/strong><\/p>\n<p>BiocManager::install(&#8216;scran&#8217;)<\/p>\n<p><strong>scran\u6807\u51c6\u5316\u6570\u636e\u4e0e\u5dee\u5f02\u5efa\u6a21<\/strong><\/p>\n<ul>\n<li><strong>\u6570\u636e\u51c6\u5907<\/strong><\/li>\n<\/ul>\n<p>\u5c0f\u679c\u5728\u8fd9\u91cc\u4f7f\u7528\u7531SingleCellExperiment\u5305\u63d0\u4f9b\u7684\u4eba\u7c7b\u80f0\u817a\u6570\u636e\u96c6\u4f5c\u4e3a\u4eca\u5929\u5e26\u7684\u6d4b\u8bd5\u6570\u636e\uff0c\u8fd9\u9700\u8981\u6211\u4eec\u5bfc\u5165scRNAseq\u5305\uff0c\u8fd8\u6ca1\u4e0b\u8f7d\u5c0f\u4f19\u4f34\u8d76\u7d27\u4e0b\u8f7d\u8d77\u6765\u54e6\uff01<\/p>\n<p>library(scRNAseq)data &lt;- GrunPancreasData()data()View(data)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"261\" class=\"wp-image-30186\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-1.png?resize=640%2C261\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-1.png?w=1174 1174w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-1.png?resize=300%2C122 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-1.png?resize=1024%2C417 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-1.png?resize=768%2C313 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-1.png?resize=600%2C244 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/> \u5bfc\u5165\u540e\uff0c\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e0b\u5bfc\u5165\u7684\u6570\u636e\u7ed3\u6784\u5427\uff01<\/p>\n<ul>\n<li><strong>\u6570\u636e\u8d28\u63a7<\/strong><\/li>\n<\/ul>\n<p>\u5728\u6807\u51c6\u5316\u4e4b\u524d\uff0c\u6211\u4eec\u9996\u5148\u5bf9\u6570\u636e\u8fdb\u884c\u4e00\u4e2a\u7b80\u5355\u7684\u7565\u5fae\u7684\u8d28\u63a7\u54e6\uff0c\u6211\u4eec\u7684\u8d28\u63a7\u5c06\u8fc7\u6ee4\u6389spike-in\u8d85\u9ad8\u4ee5\u53cacounts\u592a\u4f4e\u7684\u7ec6\u80de\u54e6\uff01<\/p>\n<p>#\u7b80\u5355\u7684\u8d28\u63a7\u53d6\u9664counts\u56fd\u7b2c\u6216\u8005spike-in\u8fc7\u9ad8\u7684\u7ec6\u80de<br \/>\nlibrary(scuttle)<br \/>\nqcdata &lt;- perCellQCMetrics(data)<br \/>\nqcftlr &lt;- quickPerCellQC(qcdata, percent_subsets=&#8221;altexps_ERCC_percent&#8221;)<br \/>\ndata &lt;- data[,!qcftlr$discard]<br \/>\nsummary(qcftlr$discard)<\/p>\n<p><strong><img decoding=\"async\" loading=\"lazy\" width=\"484\" height=\"90\" class=\"wp-image-30187\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-2.png?resize=484%2C90\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-2.png?w=484 484w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-2.png?resize=300%2C56 300w\" sizes=\"(max-width: 484px) 100vw, 484px\" data-recalc-dims=\"1\" \/><\/strong><\/p>\n<ul>\n<li><strong>\u6570\u636e\u6807\u51c6\u5316<\/strong><\/li>\n<\/ul>\n<p>\u5728\u6211\u4eec\u8fdb\u884c\u6570\u636e\u6807\u51c6\u5316\u5904\u7406\u4e4b\u524d\uff0c\u5c0f\u679c\u7ed9\u5927\u5bb6\u7b80\u5355\u7684\u79d1\u666e\u4ee5\u4e0bscran\u8fdb\u884c\u6570\u636e\u6807\u51c6\u5316\u5904\u7406\u7684\u6574\u4f53\u601d\u8def\u5427\uff01<\/p>\n<p>scran\u4e2d\u7684\u6807\u51c6\u5316\u4f1a\u4f7f\u7528\u5230computeSumFactors()\u51fd\u6570\uff0c\u8be5\u51fd\u6570\u7684\u601d\u8def\u4f7f\u7528\u4e86\u201c\u53cd\u5377\u79ef\u201d\u7684\u65b9\u6cd5\u3002\u9488\u5bf9\u5355\u7ec6\u80de\u6d4b\u5e8f\u7684dropout\u548c0\u8ba1\u6570\u73b0\u8c61\uff0cscran\u901a\u8fc7\u5408\u5e76 (pool) \u603b\u8ba1\u6570\u7c7b\u4f3c\u7684\u7ec6\u80de\uff0c\u901a\u8fc7\u5b83\u4eec\u7684\u8ba1\u6570\u603b\u548c\u6765\u4f30\u7b97\u4e00\u4e2asize factor\uff0c\u7136\u540e\u5c06\u5176\u8fdb\u4e00\u6b65\u5206\u89e3\uff0c\u6700\u540e\u7528\u5230\u6bcf\u4e2a\u7ec6\u80de\u8868\u8fbe\u8c31\u7684\u6807\u51c6\u5316\u4e2d\u3002<\/p>\n<p>\u63a5\u4e0b\u6765\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5177\u4f53\u7684\u4ee3\u7801\u5982\u4f55\u64cd\u4f5c\u5427\uff01<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"73\" class=\"wp-image-30188\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-3.png?resize=640%2C73\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-3.png?w=879 879w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-3.png?resize=300%2C34 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-3.png?resize=768%2C87 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-3.png?resize=600%2C68 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/> #\u6570\u636e\u6807\u51c6\u5316<br \/>\nlibrary(scran)<br \/>\nclutrs &lt;- quickCluster(data)<br \/>\ndata &lt;- computeSumFactors(data,clusters=clutrs)<br \/>\nsummary(sizeFactors(data))<\/p>\n<ul>\n<li><strong>\u5dee\u5f02\u5efa\u6a21<\/strong><\/li>\n<\/ul>\n<p>\u57fa\u4e8e\u4e0a\u9762\u6570\u636e\u7684\u6807\u51c6\u5316\u5904\u7406\uff0c\u6211\u4eec\u73b0\u5728\u53ef\u4ee5\u5bf9\u6570\u636e\u8fdb\u884c\u5dee\u5f02\u5316\u5efa\u6a21\u5e76\u53ef\u89c6\u5316\u5904\u7406\u5566\uff0c\u8fd8\u662f\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e0b\u5982\u4f55\u64cd\u4f5c\u5427\uff01~<\/p>\n<p>\u63a5\u4e0b\u6765\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5177\u4f53\u7684\u4ee3\u7801\u5982\u4f55\u64cd\u4f5c\u5427\uff01<\/p>\n<p>#\u6570\u636e\u6807\u51c6\u5316<br \/>\nlibrary(scran)<br \/>\nclutrs &lt;- quickCluster(data)<br \/>\ndata &lt;- computeSumFactors(data,clusters=clutrs)<br \/>\nsummary(sizeFactors(data))<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"437\" class=\"wp-image-30189\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?resize=640%2C437\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?w=2500 2500w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?resize=300%2C205 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?resize=1024%2C699 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?resize=768%2C524 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?resize=1536%2C1049 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?resize=2048%2C1398 2048w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?resize=600%2C410 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?w=1280 1280w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-4.png?w=1920 1920w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/> <img decoding=\"async\" loading=\"lazy\" width=\"1\" height=\"1\" class=\"wp-image-30190\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30185-5.png?resize=1%2C1\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u73b0\u5728\u6211\u4eec\u5c31\u5f97\u5230\u4e86\u6570\u636e\u7684\u5dee\u5f02\u6a21\u578b\u8868\u8fbe\u56fe\uff0c\u90a3\u4e48\u5982\u4f55\u5206\u6790\u8fd9\u4e2a\u56fe\u7684\u7edf\u8ba1\u7ed3\u679c\u5462\uff1f\u5c0f\u679c\u6765\u7ed9\u5927\u5bb6\u7b80\u5355\u5730\u505a\u4e2a\u89e3\u91ca\u5427\uff01<\/p>\n<p>\u9996\u5148\uff0c\u6211\u4eec\u7edf\u8ba1\u5f97\u5230\u4e86\u6bcf\u4e2a\u7ec6\u80de\u8868\u8fbe\u5730\u5e73\u5747\u503c\uff0c\u4e3a\u4e86\u65b9\u4fbf\u8ba1\u7b97\u7edf\u8ba1\uff0c\u6211\u4eec\u5c06\u4ed6\u4eec\u53d6\u5bf9\u6570\u5904\u7406\uff0cy\u8f74\u6307\u7684\u5c31\u662f\u7ec6\u80de\u4e4b\u95f4\u7684\u5dee\u5f02\u503c\uff0c\u503c\u8d8a\u5927\uff0c\u5dee\u5f02\u6027\u8d8a\u5f3a\u3002\u4ece\u56fe\u4e2d\u53ef\u4ee5\u770b\u5230\uff0c\u6709\u5c11\u91cf\u7684\u7ec6\u80de\u5206\u6563\u5728\u4e0a\u65b9\uff0c\u4f46\u662f\u5927\u90e8\u5206\u7ec6\u80de\u7684\u5dee\u5f02\u503c\u57fa\u672c\u90fd\u4fdd\u6301\u57280~5\u4e4b\u95f4\uff0c\u6574\u4f53\u7684\u5dee\u5f02\u53d8\u5316\u8d8b\u52bf\u5448\u5e73\u7f13\u72b6\u6001\u3002\u600e\u4e48\u6837\uff0c\u4f60\u770b\u61c2\u8fd9\u4e2a\u7ed3\u679c\u5206\u6790\u56fe\u4e86\u561b\uff1f<\/p>\n<p>\u597d\u5566\uff0c\u4eca\u5929\u7684\u53ef\u89c6\u5316\u5de5\u5177\u4f60\u5b66\u4f1a\u4e86\u561b\uff01\uff1f\u66f4\u591a\u751f\u4fe1\u5c0f\u5de5\u5177\u7684\u5b66\u4e60\u5c31\u8bf7\u7ee7\u7eed\u5173\u6ce8\u5c0f\u679c\u5427\uff01\u4e0b\u671f\u6211\u4eec\u4e0d\u89c1\u4e0d\u6563\uff01~~<\/p>\n","protected":false},"excerpt":{"rendered":"<p>scran\uff1a\u7ec6\u80de\u8868\u8fbe\u5927\u6570\u636e\u7684\u667a\u80fd\u5904\u7406\u5de5\u5177\uff0c\u52a9\u4f60\u6210\u4e3a\u8868\u8fbe\u5206\u6790\u4e13\u5bb6\uff01 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[&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30185"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=30185"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30185\/revisions"}],"predecessor-version":[{"id":30191,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30185\/revisions\/30191"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30185"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=30185"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=30185"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}