{"id":66543,"date":"2026-11-15T20:15:00","date_gmt":"2026-11-15T12:15:00","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=66543"},"modified":"2026-11-15T14:01:10","modified_gmt":"2026-11-15T06:01:10","slug":"rental-q013-a","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/rental-q013-a\/","title":{"rendered":"\u5b9a\u4f4dSCTransform\u5185\u5b58\u5cf0\u503c\u5e76\u68c0\u67e5\u5b9e\u73b0\u4e0e\u53c2\u6570"},"content":{"rendered":"<p><!-- ysx-rental-campaign:rental-tutorials-400-20261114 article:rental_q013_a --><\/p>\n<div class=\"ysx-rental-tutorial\">\n<figure class=\"ysx-tutorial-figure\"><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2026\/11\/rental_q013_a-poster.png?resize=1200%2C720&#038;ssl=1\" alt=\"SCTransform\u5148\u5b9a\u4f4d\u5cf0\u503c\u9636\u6bb5\uff1a\u8bb0\u5f55\u7248\u672c\u4e0ecounts\u6765\u6e90\uff1b\u8fa8\u8ba4\u62df\u5408\u548c\u6b8b\u5dee\u9636\u6bb5\uff1b\u9a8c\u8bc1\u660e\u786e\u7684\u5185\u5b58\u7b56\u7565\uff1b\u6838\u5bf9SCT\u8f93\u51fa\u518d\u8bc4\u4f30\u8d44\u6e90\" width=\"1200\" height=\"720\" loading=\"lazy\"><figcaption>\u672c\u6587\u64cd\u4f5c\u4e0e\u68c0\u67e5\u8def\u5f84\u793a\u610f\u3002<\/figcaption><\/figure>\n<p>SCTransform\u5728\u62df\u5408\u3001\u8ba1\u7b97\u6b8b\u5dee\u6216\u6574\u7406\u8f93\u51fa\u65f6\u53ef\u80fd\u8868\u73b0\u51fa\u4e0d\u540c\u7684\u5185\u5b58\u9ad8\u5cf0\u3002\u9047\u5230\u5206\u914d\u5931\u8d25\u65f6\uff0c\u5148\u786e\u5b9a\u5b83\u53d1\u751f\u5728\u54ea\u4e00\u6b65\u3001\u6570\u636e\u5982\u4f55\u5b58\u653e\u4ee5\u53ca\u8c03\u7528\u4e86\u54ea\u4e00\u5957\u5b9e\u73b0\u3002\u53ea\u63d0\u9ad8\u4e00\u4e2a\u4e0a\u9650\u6216\u5220\u9664\u51e0\u4efd\u7ed3\u679c\uff0c\u53ef\u80fd\u6ca1\u6709\u89e6\u53ca\u771f\u6b63\u9700\u8981\u5206\u914d\u7684\u5927\u5bf9\u8c61\u3002<\/p>\n<p>\u672c\u6587\u4f7f\u7528Seurat\u7684RNA\u539f\u59cbUMI counts\u4f5c\u4e3a\u8f93\u5165\uff0c\u91cd\u70b9\u662fSCTransform\u672c\u8eab\u7684\u8bca\u65ad\u3002\u5b98\u7f51\u5f53\u524d\u53c2\u8003\u9875\u4e0e\u65e7\u6559\u7a0b\u7684\u9ed8\u8ba4\u53c2\u6570\u548c\u5185\u90e8\u5b9e\u73b0\u53ef\u80fd\u4e0d\u540c\uff0c\u5e94\u4ee5\u4f60\u5b89\u88c5\u7684Seurat\u3001SeuratObject\u548csctransform\u7248\u672c\u4e3a\u51c6\u3002\u4e0d\u8981\u5c06SCT\u6821\u6b63\u540e\u7684counts\u518d\u8bef\u5f53\u4f5c\u672a\u5904\u7406\u539f\u59cb\u8ba1\u6570\u91cd\u590d\u5efa\u6a21\u3002<\/p>\n<h2>\u4fdd\u5b58\u8c03\u7528\u4fe1\u606f\uff0c\u5e76\u786e\u8ba4\u77e9\u9635\u6765\u6e90<\/h2>\n<p>\u5148\u5728\u4e0d\u6267\u884c\u5927\u8ba1\u7b97\u7684\u60c5\u51b5\u4e0b\u8bb0\u5f55\u7248\u672c\u3001assay\u7c7b\u3001counts\u5c42\u6570\u91cf\u3001\u7ec6\u80de\u6570\u3001\u7279\u5f81\u6570\u4e0e\u77e9\u9635\u7c7b\u3002\u5982\u679c\u6709\u591a\u4e2acounts\u5c42\uff0c\u5e94\u660e\u786e\u5b83\u4eec\u5bf9\u5e94\u54ea\u4e9b\u6837\u672c\u3002\u73b0\u884c\u5de5\u4f5c\u6d41\u53ef\u4ee5\u5bf9\u4e0d\u540c\u5c42\u5206\u522b\u5efa\u6a21\uff0c\u4f46\u6700\u540e\u6574\u7406\u7ed3\u679c\u4ecd\u53ef\u80fd\u4ea7\u751f\u65b0\u7684\u5185\u5b58\u9700\u6c42\uff1b\u4e0d\u5e94\u4ec5\u770b\u5355\u5c42\u5c3a\u5bf8\u5c31\u4f30\u8ba1\u6574\u4e2a\u5bf9\u8c61\u3002<\/p>\n<pre><code class=\"language-r\">library(Seurat)\nlibrary(SeuratObject)\nobj &lt;- readRDS(&quot;rna-counts.rds&quot;)\nprint(sapply(c(&quot;Seurat&quot;, &quot;SeuratObject&quot;, &quot;sctransform&quot;),\n             function(p) as.character(packageVersion(p))))\nprint(class(obj[[&quot;RNA&quot;]]))\nlayers &lt;- grep(&quot;^counts($|\\.)&quot;, Layers(obj[[&quot;RNA&quot;]]), value = TRUE)\nfor (ly in layers) {\n  m &lt;- LayerData(obj, assay = &quot;RNA&quot;, layer = ly)\n  print(list(layer = ly, dim = dim(m), class = class(m)))\n}\nwriteLines(capture.output(sessionInfo()), &quot;sct-session.txt&quot;)<\/code><\/pre>\n<table>\n<thead>\n<tr>\n<th>\u5931\u8d25\u6216\u5360\u7528\u53d1\u751f\u7684\u9636\u6bb5<\/th>\n<th>\u5e94\u68c0\u67e5\u4ec0\u4e48<\/th>\n<th>\u4e0d\u5e94\u76f4\u63a5\u4f5c\u51fa\u7684\u5224\u65ad<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>\u5bfc\u51fa\u5e76\u884c\u53d8\u91cf\u524d<\/td>\n<td>\u5b8c\u6574\u9519\u8bef\u3001worker\u6570\u548c\u5bf9\u8c61\u5927\u5c0f<\/td>\n<td>\u5bfc\u51fa\u4e0a\u9650\u62a5\u9519\u5c31\u4ee3\u8868\u7269\u7406\u5185\u5b58\u4e0d\u8db3<\/td>\n<\/tr>\n<tr>\n<td>\u6a21\u578b\u62df\u5408<\/td>\n<td>\u539f\u59cb\u8f93\u5165\u3001\u5b9e\u73b0\u3001\u6837\u672c\u4e0e\u62df\u5408\u8bbe\u7f6e<\/td>\n<td>\u6539\u53d8\u62df\u5408\u7ec6\u80de\u6570\u7b49\u4e8e\u5220\u9664\u603b\u7ec6\u80de<\/td>\n<\/tr>\n<tr>\n<td>\u6b8b\u5dee\u76f8\u5173\u6b65\u9aa4<\/td>\n<td>\u6b8b\u5dee\u7279\u5f81\u8303\u56f4\u4e0e\u5185\u5b58\u7b56\u7565<\/td>\n<td>\u6700\u7ec8\u53ea\u7559\u53d8\u5f02\u57fa\u56e0\u5c31\u6ca1\u6709\u4e2d\u95f4\u5cf0\u503c<\/td>\n<\/tr>\n<tr>\n<td>\u591a\u5c42\u7ed3\u679c\u6574\u7406<\/td>\n<td>\u5404\u5c42\u7ec6\u80de\u96c6\u5408\u4e0e\u6700\u7ec8\u8f93\u51fa<\/td>\n<td>\u5355\u5c42\u8dd1\u901a\u5c31\u610f\u5473\u7740\u603b\u5bf9\u8c61\u80fd\u5bb9\u7eb3<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h2>\u660e\u786e\u53c2\u6570\u5f71\u54cd\u7684\u662f\u54ea\u4e00\u6bb5<\/h2>\n<p><code>ncells<\/code>\u7528\u4e8e\u6a21\u578b\u62df\u5408\u4e2d\u7684\u7ec6\u80de\u62bd\u6837\uff0c\u4e0d\u5e94\u88ab\u5f53\u6210\u6700\u7ec8\u8f93\u51fa\u7ec6\u80de\u6570\u7684\u76f4\u63a5\u5f00\u5173\u3002<code>return.only.var.genes<\/code>\u7ea6\u675f\u6b8b\u5dee\u7ed3\u679c\u4fdd\u7559\u7684\u7279\u5f81\u8303\u56f4\uff0c\u800c\u4e0d\u662f\u627f\u8bfa\u6bcf\u4e00\u6b65\u90fd\u4e0d\u751f\u6210\u8f83\u5927\u4e34\u65f6\u5bf9\u8c61\u3002\u5f53\u524d\u6587\u6863\u4e2d\u7684<code>conserve.memory<\/code>\u63d0\u4f9b\u53e6\u4e00\u79cd\u51cf\u5c11\u5b8c\u6574\u6b8b\u5dee\u7269\u5316\u7684\u7b56\u7565\uff0c\u4f46\u53ef\u80fd\u9700\u8981\u66f4\u591a\u8fd0\u884c\u65f6\u95f4\uff0c\u5e76\u8981\u6c42\u76f8\u5e94\u8f93\u51fa\u8303\u56f4\u3002<\/p>\n<p>\u8fd8\u6709\u4e00\u4e9b\u5185\u90e8\u53c2\u6570\u53ea\u670d\u52a1\u4e8e\u7279\u5b9a\u591a\u5c42\u8c03\u7528\u8def\u5f84\uff0c\u4e0d\u80fd\u4ece\u51fd\u6570\u5e2e\u52a9\u4e2d\u770b\u5230\u5c31\u5f53\u4f5c\u6240\u6709\u7248\u672c\u901a\u7528\u7684\u4f18\u5316\u9009\u9879\u3002\u6bd4\u5982\u5ef6\u8fdf\u6b8b\u5dee\u6784\u5efa\u4e0e\u5177\u4f53\u65b9\u6cd5\u6709\u5173\uff0c\u5e94\u5148\u6cbf\u5f53\u524d\u516c\u5f00\u5de5\u4f5c\u6d41\u9a8c\u8bc1\u3002\u53c2\u6570\u8c03\u6574\u9700\u8981\u4e0e\u540e\u7eed\u5206\u6790\u6240\u9700\u7684\u7279\u5f81\u548c\u6a21\u578b\u4fdd\u6301\u4e00\u81f4\u3002<\/p>\n<h2>\u4ece\u5355\u5c42\u3001\u4e32\u884c\u548c\u660e\u786e\u8f93\u51fa\u8303\u56f4\u5f00\u59cb\u9a8c\u8bc1<\/h2>\n<p>\u4e0b\u4f8b\u9488\u5bf9\u6070\u6709\u4e00\u4e2aRNA counts\u5c42\u3001\u51c6\u5907\u91cd\u505aSCT\u7684\u8f93\u5165\u3002\u82e5\u6709\u591a\u5c42\u4f1a\u505c\u6b62\uff0c\u8981\u6c42\u5148\u786e\u8ba4\u5efa\u6a21\u8def\u5f84\u3002\u7279\u5f81\u6570\u53ea\u662f\u793a\u4f8b\u8bbe\u7f6e\uff0c\u5e94\u4e0e\u7814\u7a76\u5206\u6790\u8ba1\u5212\u4e00\u81f4\uff1b\u5b83\u4e0d\u4f1a\u4fdd\u8bc1\u6240\u6709\u6570\u636e\u90fd\u80fd\u5728\u67d0\u79cd\u56fa\u5b9a\u5185\u5b58\u4e2d\u8fd0\u884c\u3002<\/p>\n<pre><code class=\"language-r\">if (length(layers) != 1L) stop(&quot;\u591acounts\u5c42\u8bf7\u5148\u6309\u5f53\u524d\u591a\u5c42SCT\u5de5\u4f5c\u6d41\u6838\u5bf9&quot;)\nif (requireNamespace(&quot;future&quot;, quietly = TRUE)) {\n  future::plan(future::sequential)\n}\nobj &lt;- SCTransform(obj, assay = &quot;RNA&quot;, vst.flavor = &quot;v2&quot;,\n                   variable.features.n = 3000,\n                   conserve.memory = TRUE,\n                   return.only.var.genes = TRUE,\n                   verbose = TRUE)\nstopifnot(&quot;SCT&quot; %in% Assays(obj))\nprint(dim(LayerData(obj, assay = &quot;SCT&quot;, layer = &quot;scale.data&quot;)))\nprint(length(VariableFeatures(obj[[&quot;SCT&quot;]])))\nsaveRDS(obj, &quot;sct-checked.rds&quot;)<\/code><\/pre>\n<p>\u901a\u8fc7\u5916\u5c42\u8d44\u6e90\u5de5\u5177\u8bb0\u5f55\u6574\u4e2aR\u8fdb\u7a0b\u5cf0\u503c\uff0c\u5e76\u4fdd\u7559\u6807\u51c6\u9519\u8bef\u65e5\u5fd7\u3002\u82e5\u672c\u673a\u7248\u672c\u4e0d\u63a5\u53d7\u793a\u4f8b\u53c2\u6570\uff0c\u5e94\u5148\u67e5\u5bf9\u5e94\u7248\u672c\u5e2e\u52a9\uff0c\u4e0d\u901a\u8fc7\u5347\u7ea7\u751f\u4ea7\u73af\u5883\u6765\u63a9\u76d6\u517c\u5bb9\u95ee\u9898\u3002\u4e32\u884c\u9a8c\u8bc1\u4e3b\u8981\u907f\u514d\u8bca\u65ad\u65f6\u53e0\u52a0\u5e76\u884c\u5bf9\u8c61\u590d\u5236\uff0c\u4e0d\u80fd\u628a\u5b83\u8bf4\u6210\u5bf9\u6240\u6709SCT\u4efb\u52a1\u90fd\u66f4\u5feb\u3002<\/p>\n<h2>\u68c0\u67e5\u7ed3\u679c\u540e\u518d\u8ba8\u8bba\u914d\u7f6e<\/h2>\n<p>\u68c0\u67e5\u7ec6\u80de\u540d\u4e0e\u5143\u6570\u636e\u662f\u5426\u4ecd\u5bf9\u5e94\u3001SCT assay\u53ca\u6240\u9700\u7279\u5f81\u662f\u5426\u5b58\u5728\u3001\u6b8b\u5dee\u7ed3\u679c\u662f\u5426\u7b26\u5408\u540e\u7eedPCA\u6216\u6574\u5408\u9700\u6c42\uff0c\u5e76\u91cd\u65b0\u8bfb\u53d6\u4fdd\u5b58\u6587\u4ef6\u3002\u82e5\u4e3b\u8981\u76ee\u6807\u8fd8\u9700\u8981\u5176\u4ed6\u57fa\u56e0\u7684\u6b8b\u5dee\uff0c\u5e94\u6309\u76f8\u5e94\u6d41\u7a0b\u51c6\u5907\uff0c\u800c\u4e0d\u662f\u628a\u5f53\u524d\u7cbe\u7b80\u7ed3\u679c\u8bf4\u6210\u5168\u7279\u5f81\u90fd\u5df2\u5b8c\u6210\u3002<\/p>\n<h2>\u8f93\u5165\u5f02\u5e38\u4e5f\u4f1a\u8ba9\u8bca\u65ad\u8d70\u9519\u65b9\u5411<\/h2>\n<p>\u786e\u8ba4RNA\u5c42\u6765\u81ea\u9884\u671f\u7684\u539f\u59cbUMI\u8ba1\u6570\uff0c\u68c0\u67e5\u662f\u5426\u8bef\u7528\u4e86\u6807\u51c6\u5316\u503c\u3001\u5176\u4ed6assay\u6216\u4e0d\u5339\u914d\u7684\u7ec6\u80de\u5c5e\u6027\u3002\u53ea\u62bd\u53d6\u5c0f\u8303\u56f4\u503c\u548c\u5143\u6570\u636e\u6838\u5bf9\uff0c\u907f\u514d\u4e3a\u4e86\u505a\u68c0\u67e5\u5148\u628a\u6574\u4e2a\u77e9\u9635\u8f6c\u6210\u7a20\u5bc6\u5f62\u5f0f\u3002\u82e5\u62df\u5408\u62a5\u544a\u6570\u636e\u3001\u7279\u5f81\u6216\u534f\u53d8\u91cf\u76f8\u5173\u9519\u8bef\uff0c\u5e94\u5148\u5904\u7406\u8fd9\u4e9b\u95ee\u9898\uff0c\u518d\u5224\u65ad\u5185\u5b58\u3002<\/p>\n<p>\u9700\u8981\u56de\u5f52\u7684\u534f\u53d8\u91cf\u4e5f\u5fc5\u987b\u6709\u6e05\u695a\u7684\u7814\u7a76\u4f9d\u636e\u548c\u6b63\u786e\u7684\u7ec6\u80de\u5bf9\u5e94\u3002\u7f3a\u5931\u5217\u3001\u7f3a\u5931\u503c\u6216\u9519\u8bef\u6837\u672c\u6620\u5c04\u4e0d\u80fd\u901a\u8fc7\u589e\u52a0\u8d44\u6e90\u89e3\u51b3\u3002\u5bf9\u6bd4\u65b0\u65e7\u811a\u672c\u65f6\uff0c\u5217\u51favst.flavor\u3001\u62df\u5408\u8bbe\u7f6e\u3001\u56de\u5f52\u9879\u4e0e\u8f93\u51fa\u7279\u5f81\u8303\u56f4\u7684\u53d8\u5316\uff1b\u5982\u679c\u8fd9\u4e9b\u90fd\u6539\u53d8\u4e86\uff0c\u5c31\u5e94\u4f5c\u4e3a\u65b0\u7684\u65b9\u6cd5\u6761\u4ef6\u8bb0\u5f55\uff0c\u4e0d\u628a\u6240\u6709\u5dee\u5f02\u89e3\u91ca\u6210\u65b0\u670d\u52a1\u5668\u5e26\u6765\u7684\u6548\u679c\u3002<\/p>\n<p>\u5f53\u7248\u672c\u3001\u8f93\u5165\u542b\u4e49\u548c\u5fc5\u8981\u53c2\u6570\u5df2\u786e\u8ba4\uff0c\u4e32\u884c\u6216\u5408\u7406\u5e76\u53d1\u4e0b\u4ecd\u5b58\u5728\u660e\u786e\u5185\u5b58\u7f3a\u53e3\uff0c\u518d\u628a\u7ec6\u80de\u91cf\u3001\u7279\u5f81\u91cf\u3001\u62a5\u9519\u9636\u6bb5\u548c\u5cf0\u503c\u65e5\u5fd7\u7528\u4e8e\u5927\u5185\u5b58CPU\u65b9\u6848\u8bc4\u4f30\u3002\u4e91\u751f\u4fe1\u53ef\u6309\u4efb\u52a1\u6c9f\u901a\u8d44\u6e90\u4e0e\u73af\u5883\u8303\u56f4\uff0c\u79df\u8d41\u4e0d\u81ea\u52a8\u5305\u542b\u65b9\u6cd5\u9009\u62e9\u6216\u5b8c\u6574\u5206\u6790\u4ea4\u4ed8\u3002<\/p>\n<h2>\u53c2\u8003\u4e0e\u7248\u672c\u6838\u5bf9<\/h2>\n<ul>\n<li><a href=\"https:\/\/satijalab.org\/seurat\/reference\/sctransform\">Seurat\uff1aSCTransform\u53c2\u8003<\/a><\/li>\n<li><a href=\"https:\/\/satijalab.org\/seurat\/articles\/sctransform_vignette.html\">Seurat\uff1aSCTransform\u5de5\u4f5c\u6d41<\/a><\/li>\n<li><a href=\"https:\/\/stat.ethz.ch\/R-manual\/R-devel\/library\/base\/html\/Memory-limits.html\">R\u5b98\u65b9\u624b\u518c\uff1a\u5185\u5b58\u9650\u5236\u4e0e\u5bf9\u8c61<\/a><\/li>\n<li><a href=\"https:\/\/www.gnu.org\/software\/time\/manual\/html_node\/Memory-Resources.html\">GNU Time\uff1a\u5185\u5b58\u8d44\u6e90\u7edf\u8ba1<\/a><\/li>\n<\/ul>\n<section class=\"ysx-tutorial-downloads\">\n<h2>\u4e0b\u8f7d\u7ec3\u4e60\u6750\u6599<\/h2>\n<p><a href=\"https:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/rental-tutorials-400\/rental_q013_a\/c0a95685c4950d57aa1b\/rental_q013_a.pdf\" download>\u4e0b\u8f7d\u6559\u7a0b PDF<\/a> \u00b7 <a href=\"https:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/rental-tutorials-400\/rental_q013_a\/dc529de4070caf0026b3\/rental_q013_a.zip\" download>\u4e0b\u8f7d\u4ee3\u7801\u4e0e\u793a\u4f8b\u6570\u636e ZIP<\/a><\/p>\n<p>\u5148\u6838\u5bf9\u5305\u5185SHA256\u6e05\u5355\uff0c\u518d\u5728\u72ec\u7acb\u76ee\u5f55\u590d\u73b0\u3002<\/p>\n<\/section>\n<section 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