{"id":60544,"date":"2024-06-17T11:31:22","date_gmt":"2024-06-17T03:31:22","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60544"},"modified":"2024-06-17T11:31:22","modified_gmt":"2024-06-17T03:31:22","slug":"%e9%80%9f%e5%ba%a6%e7%9c%8b%e8%bf%87%e6%9d%a5%ef%bc%81%e5%b0%8f%e6%9e%9c%e6%95%99%e4%bd%a0%e5%ad%a6%e4%b9%a0rna%e9%80%9f%e5%ba%a6%e5%88%86%e6%9e%90r%e5%8c%85velociraptor%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60544","title":{"rendered":"\u901f\u5ea6\u770b\u8fc7\u6765\uff01\u5c0f\u679c\u6559\u4f60\u5b66\u4e60RNA\u901f\u5ea6\u5206\u6790R\u5305velociraptor\uff01"},"content":{"rendered":"


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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\">2023-12-06 19:02:40<\/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=2821072943068839938#wechat_redirect\" title=\"\u751f\u4fe1\u7ed8\u56fe\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u7ed8\u56fe<\/a><\/p>\n<\/div>\n<p style=\"margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;text-align: justify;\" data-mpa-powered-by=\"yiban.io\"><span style=\"font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100012865\" data-ratio=\"0.23333333333333334\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_rE2v0O5WiaUDJjgv5bxK2G1ePHyH2g-77.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"color: rgb(32, 33, 34);font-size: 15px;text-wrap: wrap;background-color: rgb(255, 255, 255);font-family: Cambria;letter-spacing: 0.578px;text-align: center;\" data-recalc-dims=\"1\"><strong><span style=\"font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;color: rgb(0, 122, 170);\">\u7b80\u4ecb<\/span><\/strong><\/span><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u9996\u5148\u5c0f\u679c\u7b80\u5355\u4ecb\u7ecd\u4e0b\u4ec0\u4e48\u662fRNA\u901f\u5ea6\uff08RNA velocity)\u3002RNA\u4e30\u5ea6\u662f\u5355\u4e2a\u7ec6\u80de\u72b6\u6001\u7684\u6709\u529b\u6307\u6807\uff0c\u5355\u7ec6\u80de RNA \u6d4b\u5e8f\u53ef\u4ee5\u4ee5\u9ad8\u5b9a\u91cf\u7cbe\u5ea6\u3001\u7075\u654f\u5ea6\u548c\u901a\u91cf\u63ed\u793a RNA \u4e30\u5ea6\u3002\u7136\u800c\uff0c\u8fd9\u79cd\u65b9\u6cd5\u4ec5\u6355\u83b7\u67d0\u4e2a\u65f6\u95f4\u70b9\u7684\u9759\u6001\u5feb\u7167\uff0c\u8fd9\u5bf9\u5206\u6790\u80da\u80ce\u53d1\u751f\u6216\u7ec4\u7ec7\u518d\u751f\u7b49\u65f6\u95f4\u5206\u8fa8\u73b0\u8c61\u63d0\u51fa\u4e86\u6311\u6218\u3002\u57282018\u5e74La Manno\u7b49\u4eba\u5f15\u5165\u4e86RNA\u901f\u5ea6(RNA velocity)\u7684\u6982\u5ff5\uff0c\u8be5\u9879\u7814\u7a76\u53d1\u8868\u5728\u4e86Nature\u4e0a\u3002\u901a\u8fc7\u5c06\u6d4b\u91cf\u7ed3\u679c\u4e0e\u6f5c\u5728\u7684mRNA\u526a\u63a5\u52a8\u529b\u5b66\u8054\u7cfb\u8d77\u6765\uff0c\u63a2\u7d22\u5b9a\u5411\u8f68\u8ff9\u7684\u63a8\u65ad\uff1a\u7279\u5b9a\u57fa\u56e0\u7684\u8f6c\u5f55\u8bf1\u5bfc\u5bfc\u81f4(\u65b0\u8f6c\u5f55\u7684)\u524d\u4f53\u672a\u526a\u63a5mRNA\u7684\u589e\u52a0\uff0c\u800c\u76f8\u53cd\uff0c\u8f6c\u5f55\u7684\u6291\u5236\u6216\u7f3a\u5931\u5bfc\u81f4\u672a\u526a\u63a5mRNA\u7684\u51cf\u5c11\u3002\u56e0\u6b64\uff0c\u901a\u8fc7\u5c06\u672a\u526a\u63a5\u7684mRNA\u4e0e\u6210\u719f\u7684\u526a\u63a5mRNA\u8fdb\u884c\u533a\u5206\uff0c\u53ef\u4ee5\u8fd1\u4f3c\u5730\u5f97\u5230mRNA\u4e30\u5ea6\u7684\u53d8\u5316\uff0c\u4e5f\u5c31\u662fmRNA\u7684\u65f6\u95f4\u5bfc\u6570\uff0c\u5373RNA\u901f\u5ea6\u3002<\/span><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: 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left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;color: rgb(0, 122, 170);\"><strong>\u672a\u526a\u63a5\u548c\u526a\u63a5 mRNA \u4e4b\u95f4\u7684\u5e73\u8861\u53ef\u9884\u6d4b\u7ec6\u80de\u72b6\u6001\u8fdb\u5c55    <\/strong><\/span><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-size: 15px;text-indent: 0pt;letter-spacing: 0.034em;\">RNA \u901f\u5ea6\u662f\u4e00\u79cd\u9ad8\u7ef4\u5411\u91cf\uff0c\u53ef\u4ee5\u9884\u6d4b\u5355\u4e2a\u7ec6\u80de\u5728\u6570\u5c0f\u65f6\u7684\u65f6\u95f4\u5c3a\u5ea6\u4e0a\u7684\u672a\u6765\u72b6\u6001\u3002<\/span><span style=\"font-size: 15px;text-indent: 0pt;letter-spacing: 0.034em;\">\u90a3RNA\u901f\u5ea6\u6709\u4ec0\u4e48\u7528\u5462\uff1f<\/span><span style=\"font-size: 15px;text-indent: 0pt;letter-spacing: 0.034em;\">RNA \u901f\u5ea6\u5c06\u6781\u5927\u5730\u5e2e\u52a9\u5206\u6790\u53d1\u80b2\u8c31\u7cfb\u548c\u7ec6\u80de\u52a8\u529b\u5b66\uff0cRNA \u901f\u5ea6\u5206\u6790\u4f7f\u6211\u4eec\u80fd\u591f\u4f7f\u7528\u8f6c\u5f55\u52a8\u529b\u5b66\u7684\u6570\u5b66\u6a21\u578b\u6765\u63a8\u65ad scRNA-seq \u5b9e\u9a8c\u4e2d\u672a\u76f4\u63a5\u89c2\u5bdf\u5230\u7684\u8f6c\u5f55\u52a8\u529b\u5b66\u3002<\/span><span style=\"font-size: 15px;text-indent: 0pt;letter-spacing: 0.034em;\"> \u6211\u4eec\u53ef\u4ee5\u4f7f\u7528 RNA \u901f\u5ea6\u6765\u786e\u5b9a\u67d0\u4e2a\u9776\u57fa\u56e0\u5728\u7ed9\u5b9a\u7684\u9776\u7ec6\u80de\u7fa4\u4e2d\u662f\u5426\u88ab\u8bf1\u5bfc\u6216\u6291\u5236\u3002<\/span><span style=\"font-size: 15px;text-indent: 0pt;letter-spacing: 0.034em;\"> \u6b64\u5916\uff0c\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7\u4f2a\u65f6\u95f4\u8f68\u8ff9\u63a8\u65ad\u8fd9\u4e9b\u4fe1\u606f\u6765\u9884\u6d4b\u7ec6\u80de\u547d\u8fd0\u7684\u51b3\u5b9a\u3002<\/span><br \/><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100012751\" data-ratio=\"0.4361111111111111\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_xHT8MDnoW5bw3nUO2eP99WJZNXDf2g.png?resize=553%2C242\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyv5Zt69WdcXZibRz9fKGian3FK0CYfyuAw332E2ibWFGZS1CdxHT8MDnoW5bw3nUO2eP99WJZNXDf2g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"242 .27001953125\" width=\"553 .739990234375\" data-recalc-dims=\"1\"><\/span><\/p>\n<p style=\"text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;text-align: justify;\"><span style=\"font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;color: rgb(0, 122, 170);\"><strong>RNA\u901f\u5ea6\u52a8\u6001\u6a21\u578b<\/strong><\/span><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u76ee\u524d\u6bd4\u8f83\u5e38\u7528\u7684\u7528\u6765\u4f5c\u4e3aRNA\u901f\u5ea6\u5206\u6790\u7684\u662f\u57fa\u4e8epython\u7684scVelo, scVelo\u662f\u57fa\u4e8epython\u7684RNA\u901f\u5ea6\u5206\u6790\u5de5\u5177\uff0c\u4f46\u662f\u6211\u4eec\u5f88\u591a\u5c0f\u4f19\u4f34\u66f4\u559c\u6b22\u4f7f\u7528R\u8bed\u8a00\uff0c\u6240\u4ee5\u5462\u4eca\u5929\u6211\u4eec\u6765\u4ecb\u7ecd\u4e0b\u521a\u53d1\u8868\u7684\u57fa\u4e8eR\u8bed\u8a00\u7684RNA\u901f\u5ea6\u5206\u6790\u8f6f\u4ef6\u5305velociraptor\uff0c\u4e0b\u9762\u8ddf\u5c0f\u679c\u4e00\u8d77\u5b66\u4e60\u5427\uff01<\/span><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u8be5\u8f6f\u4ef6\u5305\u5728 Bioconductor SingleCellExperiment \u6570\u636e\u7ed3\u6784\u548c scvelo Python \u8f6f\u4ef6\u5305\u4e4b\u95f4\u63d0\u4f9b\u4e86\u4e00\u4e2a\u8f7b\u91cf\u7ea7\u63a5\u53e3\uff0c\u7528\u4e8e RNA \u901f\u5ea6\u8ba1\u7b97\u3002\u8be5\u754c\u9762\u4e0e\u8bb8\u591a\u5176\u4ed6 SingleCellExperiment \u517c\u5bb9\u529f\u80fd\u7684\u754c\u9762\u76f8\u5f53\uff0c\u5141\u8bb8\u7528\u6237\u5c06 RNA \u901f\u5ea6\u8ba1\u7b97\u63d2\u5165\u73b0\u6709\u7684 Bioconductor \u5206\u6790\u6846\u67b6\u4e2d\u3002\u4e3a\u4e86\u8fdb\u884c\u6f14\u793a\uff0c\u6211\u4eec\u5c06\u4f7f\u7528 Hermann \u7b49\u4eba\u7684\u6570\u636e\u96c6(2018)\uff0c\u901a\u8fc7 scRNAseq \u5305\u63d0\u4f9b\u3002\u8be5\u6570\u636e\u96c6\u5305\u542b 2,325 \u4e2a\u5c0f\u9f20\u751f\u7cbe\u7ec6\u80de\u7684\u526a\u63a5\u548c\u672a\u526a\u63a5 UMI \u8ba1\u6570\u7684\u57fa\u56e0\u4f30\u8ba1\u3002<\/span>    <\/span><o:page><\/o:page><\/p>\n<p style=\"text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;text-align: justify;\"><span style=\"font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;color: rgb(0, 122, 170);\"><strong>\u5bfc\u5165\u6570\u636e<\/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<\/ul>\n<pre class=\"code-snippet__js\"><code><span class=\"code-snippet_outer\">library(scRNAseq)<\/span><\/code><code><span class=\"code-snippet_outer\">sce<-HermannSpermatogenesisData()<span style=\"color: rgb(255, 255, 255);font-family: Menlo;font-size: 15px;background-color: rgb(0, 0, 0);text-indent: 0pt;letter-spacing: 0.034em;\"><\/span><\/span><\/code><\/pre>\n<\/section>\n<h1 style=\"text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;text-align: justify;\"><span style=\"font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;color: rgb(0, 122, 170);\"><strong>\u53d6\u6837\u793a\u8303<br \/>\n  <\/strong><\/span><\/h1>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5b8c\u6574\u7684\u6570\u636e\u96c6\u9700\u8981\u9ad8\u8fbe 12 GB \u7684\u5185\u5b58\u624d\u80fd\u7528\u4e8e\u6b64\u63d2\u56fe\u4e2d\u5448\u73b0\u7684\u793a\u4f8b\u7528\u6cd5\u3002\u51fa\u4e8e\u6f14\u793a\u76ee\u7684\uff0c\u5c0f\u679c\u5c06\u6570\u636e\u96c6\u4e0b\u91c7\u6837\u5230\u524d 500 \u4e2a\u5355\u5143\u683c\u3002\u5982\u679c\u60a8\u6709\u8db3\u591f\u7684\u5185\u5b58\uff0c\u8bf7\u968f\u610f\u8df3\u8fc7\u6b64\u4e0b\u91c7\u6837\u6b65\u9aa4\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u53d6\u6837500\u4e2a\u7ec6\u80de<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">sce<\/span><-sce[, 1:500]<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">          <o:p> <\/o:p><\/span><span style=\"font-size: 15px;text-indent: 0pt;letter-spacing: 0.034em;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100012866\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-10.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"color: rgb(51, 51, 51);font-weight: 700;letter-spacing: 0.578px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;text-align: center;\" data-recalc-dims=\"1\"><\/span><span style=\"font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;font-weight: bold;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;font-size: 15px;color: rgb(0, 122, 170);\"><strong>\u57fa\u672c\u5de5\u4f5c\u6d41\u7a0b   <\/strong><\/span><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u9009\u62e9\u524d2000\u4e2a\u57fa\u56e0\u3002<\/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=\"go\"><code><span class=\"code-snippet_outer\">library(scuttle)<\/span><\/code><code><span class=\"code-snippet_outer\">sce<-logNormCounts(sce, assay.<span class=\"code-snippet__keyword\">type<\/span>=<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">library(scran)<\/span><\/code><code><span class=\"code-snippet_outer\">dec<-modelGeneVar(sce)<\/span><\/code><code><span class=\"code-snippet_outer\">top.hvgs<-getTopHVGs(dec, n=<span class=\"code-snippet__number\">2000<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">scvelo() \u4f7f\u7528\u7a33\u6001\u65b9\u6cd5\u6765\u4f30\u8ba1\u901f\u5ea6\uff0c\u4f46\u4e5f\u53ef\u4ee5\u901a\u8fc7\u4fee\u6539\u6a21\u5f0f\u53c2\u6570\u6765\u4f7f\u7528 scvelo \u4e2d\u5b9e\u73b0\u7684\u968f\u673a\u548c\u52a8\u6001\u6a21\u578b\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\">library(velociraptor)<\/span><\/code><code><span class=\"code-snippet_outer\">velo.<span class=\"code-snippet__keyword\">out<\/span><-scvelo(sce, subset.row=top.hvgs, assay.X=<span class=\"code-snippet__string\">\"spliced\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">velo.<span class=\"code-snippet__keyword\">out<\/span> <\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u4e0a\u9762\u7684\u8c03\u7528\u4e2d\uff0c\u6211\u4eec\u4f7f\u7528”\u62fc\u63a5”\u8ba1\u6570\u77e9\u9635\u4f5c\u4e3a\u5178\u578b\u5916\u663e\u5b50\u8ba1\u6570\u77e9\u9635\u7684\u4ee3\u7406\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\">library(scater)<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(100)<\/span><\/code><code><span class=\"code-snippet_outer\">sce<-runPCA(sce, subset_row=top.hvgs)<\/span><\/code><code><span class=\"code-snippet_outer\">sce<-runTSNE(sce, dimred=<span class=\"code-snippet__string\">\"PCA\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">sce<span class=\"code-snippet__variable\">$velocity_pseudotime<\/span><-velo.out<span class=\"code-snippet__variable\">$velocity_pseudotime<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plotTSNE(sce, colour_by=<span class=\"code-snippet__string\">\"velocity_pseudotime\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100012750\" data-ratio=\"0.6175925925925926\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_a2xrg2RRPuXGmgibGpSiaic2wLWXtg.png?resize=553%2C341\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyv5Zt69WdcXZibRz9fKGian3yGypIBpU4gqcnMgDSNibG7VEuyRHia2xrg2RRPuXGmgibGpSiaic2wLWXtg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"341 .94000244140625\" width=\"553 .739990234375\" data-recalc-dims=\"1\"><\/span><span style=\"font-size: 15px;\">    <\/span><o:page><\/o:page><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5c06\u901f\u5ea6\u5411\u91cf\u5d4c\u5165\u5230\u6211\u4eec\u60f3\u8981\u7684\u4f4e\u7ef4\u7a7a\u95f4\u4e2d\u4e5f\u5f88\u7b80\u5355\uff0c\u5982\u4e0b\u9762\u7684 t-SNE \u5750\u6807: \u8fd9\u79cd\u65b9\u6cd5\u4f7f\u7528\u57fa\u4e8e\u7f51\u683c\u7684\u65b9\u6cd5\u5c06\u6bcf\u4e2a\u5355\u5143\u7684\u5411\u91cf\u6c47\u603b\u4e3a\u5f53\u5730\u4ee3\u8868\uff0c\u4ee5\u4fbf\u6709\u6548\u5730\u53ef\u89c6\u5316\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"ruby\"><code><span class=\"code-snippet_outer\">embedded<-embedVelocity(reducedDim(sce, <span class=\"code-snippet__string\">\"TSNE\"<\/span>), velo.out)<\/span><\/code><code><span class=\"code-snippet_outer\">grid.df<-gridVectors(sce, embedded, use.dimred=<span class=\"code-snippet__string\">\"TSNE\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">library(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\">plotTSNE(sce, colour_by=<span class=\"code-snippet__string\">\"velocity_pseudotime\"<\/span>) +<\/span><\/code><code><span class=\"code-snippet_outer\"> geom_segment(data=grid.df, mapping=aes(x=start.<span class=\"code-snippet__number\">1<\/span>, y=start.<span class=\"code-snippet__number\">2<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> xend=<span class=\"code-snippet__keyword\">end<\/span>.<span class=\"code-snippet__number\">1<\/span>, yend=<span class=\"code-snippet__keyword\">end<\/span>.<span class=\"code-snippet__number\">2<\/span>, colour=NULL), arrow=arrow(length=unit(<span class=\"code-snippet__number\">0<\/span>.<span class=\"code-snippet__number\">05<\/span>, <span class=\"code-snippet__string\">\"inches\"<\/span>)))<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 0pt;line-height: normal;font-size: 12pt;font-family: \u5b8b\u4f53;font-weight: normal;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100012749\" data-ratio=\"0.6175925925925926\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_MSTmJB7buuC7NQQDAVSBmcwS5RSjHw.png?resize=553%2C341\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyv5Zt69WdcXZibRz9fKGian3eQMK8k61z9joIUDozlJzNB3QMSTmJB7buuC7NQQDAVSBmcwS5RSjHw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"341 .94000244140625\" width=\"553 .739990234375\" data-recalc-dims=\"1\"><\/span><\/p>\n<p style=\"text-align: justify;margin-left: 0pt;text-indent: 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