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<\/span><span class=\"rich_media_meta 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\">2023-10-16 19:00:07<\/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=3142533467331887107#wechat_redirect\" title=\"\u5355\u7ec6\u80de\u6d4b\u5e8f\" target=\"_blank\" rel=\"noopener\">#\u5355\u7ec6\u80de\u6d4b\u5e8f<\/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><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 data-mpa-powered-by=\"yiban.io\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">hello\uff0c\u4f60\u77e5\u9053\u6709\u4e00\u4e2aR\u5305\u53ef\u4ee5\u751f\u6210\u6a21\u62df\u5355\u7ec6\u80deRNA-seq\u7684\u6570\u636e\uff0c\u5e76\u53ef\u4ee5\u7528\u4e8e\u8bc4\u4f30\u548c\u6bd4\u8f83\u4e0d\u540c\u7684\u5206\u6790\u65b9\u6cd5\u561b\uff1f\u4eca\u5929\u5c0f\u679c\u5c31\u6765\u6559\u5927\u5bb6\u5982\u4f55\u4f7f\u7528\u8fd9\u4e2aR\u5305\uff0c\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u770b\u4e0b\u53bb\u5427\uff01<\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 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\/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"font-size: 14px;letter-spacing: 0.034em;\">splatter\u662f\u4e00\u4e2a\u7528\u4e8e\u6a21\u62df\u548c\u5206\u6790\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\u7684R\u8bed\u8a00\u5305\u3002\u5b83\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u529f\u80fd\uff0c\u4f7f\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u751f\u6210\u6a21\u62df\u6570\u636e\u3001\u8fdb\u884c\u53c2\u6570\u4f30\u8ba1\u3001\u6570\u636e\u6807\u51c6\u5316\u3001\u964d\u7ef4\u5206\u6790\u7b49\u3002\u4e0b\u9762\u5c0f\u679c\u6765\u4ecb\u7ecd\u4e00\u4e0bsplatter\u5305\u7684\u4e3b\u8981\u529f\u80fd\u548c\u4f5c\u7528\uff1a<br \/><\/span><\/p>\n<ol class=\"list-paddingleft-1\">\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\"><strong>\u6a21\u62df\u6570\u636e\u751f\u6210\uff1a<\/strong>splatter\u5141\u8bb8\u7528\u6237\u6839\u636e\u81ea\u5b9a\u4e49\u7684\u53c2\u6570\u751f\u6210\u6a21\u62df\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\"><strong>\u53c2\u6570\u4f30\u8ba1\uff1a<\/strong>splatter\u63d0\u4f9b\u4e86\u529f\u80fd\u5f3a\u5927\u7684\u53c2\u6570\u4f30\u8ba1\u65b9\u6cd5\uff0c\u53ef\u4ee5\u4ece\u7ed9\u5b9a\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u4e2d\u4f30\u8ba1\u51fa\u6a21\u578b\u7684\u53c2\u6570\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 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14px;\"><strong>\u6570\u636e\u53ef\u89c6\u5316\uff1a<\/strong>splatter\u63d0\u4f9b\u4e86\u591a\u79cd\u7ed8\u56fe\u51fd\u6570\uff0c\u7528\u4e8e\u53ef\u89c6\u5316\u6a21\u62df\u6570\u636e\u3001\u53c2\u6570\u4f30\u8ba1\u7ed3\u679c\u3001\u6807\u51c6\u5316\u540e\u7684\u6570\u636e\u3001\u964d\u7ef4\u5206\u6790\u7ed3\u679c\u7b49\u3002<\/span><\/p>\n<\/li>\n<\/ol>\n<p><span style=\"font-size: 14px;\">\u603b\u800c\u8a00\u4e4b\uff0csplatter\u662f\u4e00\u4e2a\u529f\u80fd\u4e30\u5bcc\u7684R\u5305\uff0c\u901a\u8fc7\u6a21\u62df\u751f\u6210\u3001\u53c2\u6570\u4f30\u8ba1\u3001\u6570\u636e\u6807\u51c6\u5316\u548c\u964d\u7ef4\u5206\u6790\u7b49\u529f\u80fd\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u66f4\u597d\u5730\u7406\u89e3\u548c\u5206\u6790\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\uff0c\u4e3a\u5355\u7ec6\u80de\u7814\u7a76\u63d0\u4f9b\u4e86\u6709\u529b\u7684\u5de5\u5177\u548c\u65b9\u6cd5\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u63a5\u4e0b\u6765\u5c0f\u679c\u5c06\u4f7f\u7528R\u8bed\u8a00\u4e2d\u7684splatter\u548cscater\u5305\u8fdb\u884c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u6a21\u62df\u548c\u5206\u6790\u3002\u90a3\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u5b66\u8d77\u6765\u5427\uff01<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3888888888888889\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"1080\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-16_\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\/1_IlmBAWe69EMUPMhNEgrv6NXX85lJxg.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwyrj7kbUR3ULG9ZUbLrLkgibzL8qUpQROfe8ebc3gNSnu1dIlmBAWe69EMUPMhNEgrv6NXX85lJxg\/640?wx_fmt=jpeg'\" \/><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">1. \u5feb\u901f\u521b\u5efa\u6a21\u62df\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u9996\u5148\u6211\u4eec\u4f7f\u7528splatter\u5305\u4e2d\u7684mockSCE\u51fd\u6570\u5feb\u901f\u521b\u5efa\u4e00\u4e2a\u6a21\u62df\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u3002mockSCE\u51fd\u6570\u53ef\u4ee5\u8bbe\u7f6e\u7ec6\u80de\u7684\u6570\u91cf\uff08ncells\uff09\u3001\u57fa\u56e0\u7684\u6570\u91cf\uff08ngenes\uff09\u548cspike-in\u7684\u6570\u91cf\uff08nspikes\uff09\uff0c\u5e76\u8fd4\u56de\u4e00\u4e2aSingleCellExperiment\uff08SCE\uff09\u5bf9\u8c61\u3002\u4ee3\u7801\u4e2d\u7684set.seed(1)\u7528\u4e8e\u8bbe\u7f6e\u968f\u673a\u6570\u79cd\u5b50\uff0c\u4fdd\u8bc1\u7ed3\u679c\u7684\u53ef\u91cd\u590d\u6027\u3002\u6700\u540e\uff0c\u6211\u4eec\u4f7f\u7528counts\u51fd\u6570\u67e5\u770b\u6a21\u62df\u6570\u636e\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u3002<\/span><br \/><\/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=\"cs\"><code><span class=\"code-snippet_outer\">library(splatter)<\/span><\/code><code><span class=\"code-snippet_outer\">library(scater)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">### 1. \u5feb\u901f\u521b\u5efa\u6a21\u62df\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\"># Usage<\/span><\/code><code><span class=\"code-snippet_outer\"># mockSCE(ncells = 200, ngenes = 2000, nspikes = 100)<\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(1)<\/span><\/code><code><span class=\"code-snippet_outer\">sce <- mockSCE() # class: SingleCellExperiment<\/span><\/code><code><span class=\"code-snippet_outer\">counts(sce)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u6a21\u62df\u751f\u6210\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff1a<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6253602305475504\" data-type=\"png\" data-w=\"1041\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-16_\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\/2_bSyY6vTZzMrIXefO6fedHjh4XzdjMA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtdVZ2CHfs2jHEP3GxxrKRBon3bSyY6vTZzMrIXefO6fedHjh4XzdjMA\/640?wx_fmt=png'\" \/><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">2. \u53c2\u6570\u4f30\u8ba1<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u4f7f\u7528splatEstimate\u51fd\u6570\u4ece\u7ed9\u5b9a\u7684\u6570\u636e\u4e2d\uff08\u8fd9\u91cc\u662f\u4e0a\u4e00\u90e8\u5206\u6a21\u62df\u751f\u6210\u7684\u6570\u636e\uff09\u4f30\u8ba1\u53c2\u6570\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\">### 2. \u53c2\u6570\u4f30\u8ba1<\/span><\/code><code><span class=\"code-snippet_outer\"># \u4ece\u6570\u636e\uff08\u6a21\u62df\u6570\u636e\u6216\u771f\u5b9e\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff09\u4e2d\u4f30\u8ba1\u53c2\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">params <- splatEstimate(sce) # Params object<\/span><\/code><\/pre>\n<\/section>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">3. \u81ea\u5b9a\u4e49\u53c2\u6570\uff0c\u521b\u5efa\u6a21\u62df\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u6765\u5b66\u4e60\u5982\u4f55\u6839\u636e\u81ea\u5b9a\u4e49\u53c2\u6570\u521b\u5efa\u6a21\u62df\u6570\u636e\u3002\u9996\u5148\uff0c\u4f7f\u7528newSplatParams\u51fd\u6570\u521b\u5efa\u4e00\u4e2a\u53c2\u6570\u5bf9\u8c61params\u3002\u7136\u540e\uff0c\u4f7f\u7528getParam\u51fd\u6570\u67e5\u770b\u53c2\u6570\u5bf9\u8c61\u4e2d\u7684\u53c2\u6570\u8bbe\u5b9a\u3002\u63a5\u4e0b\u6765\uff0c\u4f7f\u7528setParam\u548csetParams\u51fd\u6570\u8bbe\u7f6e\u53c2\u6570\u5bf9\u8c61\u4e2d\u7684\u53c2\u6570\u3002\u6700\u540e\uff0c\u4f7f\u7528splatSimulate\u51fd\u6570\u6839\u636e\u53c2\u6570\u5bf9\u8c61\u521b\u5efa\u6a21\u62df\u6570\u636e\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<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\">### 3. \u81ea\u5b9a\u4e49\u53c2\u6570\uff0c\u521b\u5efa\u6a21\u62df\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\"># \u521b\u5efa\u53c2\u6570\u5bf9\u8c61<\/span><\/code><code><span class=\"code-snippet_outer\">params <- newSplatParams() #\u9ed8\u8ba410000 Genes\uff0c100 Cells<\/span><\/code><code><span class=\"code-snippet_outer\"># \u67e5\u770b\u53c2\u6570\u5bf9\u8c61\u4e2d\u7684\u53c2\u6570\u8bbe\u5b9a<\/span><\/code><code><span class=\"code-snippet_outer\">getParam(params, \"nGenes\")<\/span><\/code><code><span class=\"code-snippet_outer\">getParam(params, \"nCells\")<\/span><\/code><code><span class=\"code-snippet_outer\">getParams(params, c(\"nGenes\", \"mean.rate\", \"mean.shape\"))<\/span><\/code><code><span class=\"code-snippet_outer\"># \u8bbe\u5b9a\u53c2\u6570\u5bf9\u8c61\u4e2d\u7684\u53c2\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParam(params, \"nGenes\", 5000)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParam(params, \"batchCells\", 50)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParams(params, mean.shape = 0.5, de.prob = 0.2)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParams(params, update = list(nGenes = 8000, mean.rate = 0.5))<\/span><\/code><\/pre>\n<\/section>\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=\"cs\"><code><span class=\"code-snippet_outer\"># \u6839\u636e\u53c2\u6570\uff0c\u521b\u5efa\u6a21\u62df\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">sim <- splatSimulate(params)<\/span><\/code><\/pre>\n<\/section>\n<p><strong><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.4609375\" data-type=\"png\" data-w=\"640\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_FMptqBicqugS405mtOSrSIdXJImiag.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtbd2Ct3ibLVHJF4rOSSSpsyib4tXcFMptqBicqugS405mtOSrSIdXJImiag\/640?wx_fmt=png'\" \/><\/strong><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">4. \u63d0\u53d6SingleCellExperiment\u7c7b\u4fe1\u606f<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4ecb\u7ecd\u63d0\u53d6SingleCellExperiment\u5bf9\u8c61\u4e2d\u7684\u4fe1\u606f\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<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=\"objectivec\"><code><span class=\"code-snippet_outer\">### 4. \u63d0\u53d6SingleCellExperiment\u7c7b\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">class(sim)<\/span><\/code><code><span class=\"code-snippet_outer\"># Information about genes<\/span><\/code><code><span class=\"code-snippet_outer\">head(rowData(sim))<\/span><\/code><code><span class=\"code-snippet_outer\"># Information about cells<\/span><\/code><code><span class=\"code-snippet_outer\">head(colData(sim))<\/span><\/code><code><span class=\"code-snippet_outer\"># Gene by cell matrices<\/span><\/code><code><span class=\"code-snippet_outer\">names(assays(sim))<\/span><\/code><code><span class=\"code-snippet_outer\"># Example of cell means matrix<\/span><\/code><code><span class=\"code-snippet_outer\">assays(sim)$CellMeans[1:5, 1:5]<\/span><\/code><code><span class=\"code-snippet_outer\"># \u8868\u8fbe\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">counts <- counts(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">counts[1:3,1:5]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">class(counts) # \"matrix\" \"array\" <\/span><\/code><code><span class=\"code-snippet_outer\">typeof(counts) # [1] \"integer\"<\/span><\/code><code><span class=\"code-snippet_outer\">dim(counts) #[1] 8000 100<\/span><\/code><\/pre>\n<\/section>\n<p><strong>\u8fd0\u884c\u7ed3\u679c\u5982\u4e0b\uff1a<\/strong><\/p>\n<p><strong><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5316804407713499\" data-type=\"png\" data-w=\"363\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_e65e7lGGgws54ibhIGiacLSGUOIuGA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtrj0GLxxNLXMNRULCEg24VYHSqqe65e7lGGgws54ibhIGiacLSGUOIuGA\/640?wx_fmt=png'\" \/><\/strong><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">5. \u6570\u636e\u6807\u51c6\u5316\uff0c\u5bf9\u6570\u5316\u548c\u964d\u7ef4<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8fdb\u4e00\u6b65\u5730\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u5982\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316\u3001\u5bf9\u6570\u5316\u548c\u964d\u7ef4\u5904\u7406\u3002\u9996\u5148\uff0c\u4f7f\u7528logNormCounts\u51fd\u6570\u5bf9SingleCellExperiment\u5bf9\u8c61\u4e2d\u7684counts\u503c\u8fdb\u884c\u5bf9\u6570\u8f6c\u6362\u548c\u5f52\u4e00\u5316\u3002\u901a\u8fc7logcounts\u51fd\u6570\u53ef\u4ee5\u67e5\u770b\u8f6c\u6362\u540e\u7684\u5bf9\u6570\u8868\u8fbe\u77e9\u9635\u3002\u7136\u540e\uff0c\u4f7f\u7528runPCA\u51fd\u6570\u5bf9\u6570\u636e\u8fdb\u884cPCA\u964d\u7ef4\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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">### 5. \u6570\u636e\u6807\u51c6\u5316\uff0c\u5bf9\u6570\u5316\u548c\u964d\u7ef4<\/span><\/code><code><span class=\"code-snippet_outer\">## {scuttle}\u5305\u7684\u51fd\u6570:logNormCounts<\/span><\/code><code><span class=\"code-snippet_outer\">## {scater}\u5305\u7684\u51fd\u6570:runPCA,plotPCA<\/span><\/code><code><span class=\"code-snippet_outer\"># SingleCellExperiment \u5bf9\u8c61\u7684counts\u503c\u8ba1\u7b97\u5bf9\u6570\u8f6c\u6362\u7684\u5f52\u4e00\u5316\u8868\u8fbe\u5f0f\u503c<\/span><\/code><code><span class=\"code-snippet_outer\">sim <- logNormCounts(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">counts(sim)[1:3,1:5]<\/span><\/code><code><span class=\"code-snippet_outer\">logcounts(sim)[1:3,1:5]<\/span><\/code><code><span class=\"code-snippet_outer\"># PCA\u964d\u7ef4<\/span><\/code><code><span class=\"code-snippet_outer\">sim <- runPCA(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6700\u540e\uff0c\u5c0f\u679c\u4f7f\u7528plotPCA\u51fd\u6570\u7ed8\u5236PCA\u964d\u7ef4\u7ed3\u679c\u3002\u6211\u4eec\u6765\u770b\u770b\u53ef\u89c6\u5316\u7684\u7ed3\u679c\u662f\u4ec0\u4e48\u6837\u5427\uff01<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9933598937583001\" data-type=\"png\" data-w=\"753\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_hE9PvQ2gr8LWsrWDzZhJhe0lmo8l0w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtrqicXPVibjHRh359yGGrxVldhhhE9PvQ2gr8LWsrWDzZhJhe0lmo8l0w\/640?wx_fmt=png'\" \/><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">6. \u521b\u5efa\u590d\u6742\u7684\u6a21\u62df\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u6700\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u521b\u5efa\u66f4\u590d\u6742\u7684\u6a21\u62df\u6570\u636e\uff0c\u5305\u62ec\u5177\u6709\u7ec4\u7ed3\u6784\u3001\u8def\u5f84\u7ed3\u6784\u548c\u6279\u6b21\u6548\u5e94\u7684\u6a21\u62df\u6570\u636e\u3002<\/span><br \/><\/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=\"cs\"><code><span class=\"code-snippet_outer\">### 6. \u521b\u5efa\u590d\u6742\u7684\u6a21\u62df\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">## groups<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- splatSimulate(group.prob = c(0.3, 0.7), method = \"groups\",<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- logNormCounts(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- runPCA(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.groups, colour_by = \"Group\")<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u6765\u770b\u770b\u964d\u7ef4\u540e\u7684\u7ed3\u679c\uff1a<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0026702269692924\" data-type=\"png\" data-w=\"749\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-16_\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\/6_u58ksB6zLNmrXWOfb7Q25GrFHgKhQg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtblCI54RiaZgHXbnQ063S3xgX5u58ksB6zLNmrXWOfb7Q25GrFHgKhQg\/640?wx_fmt=png'\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">dim(counts(sim.groups))<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.groups)$DEFacGroup1<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.groups)$DEFacGroup2<\/span><\/code><code><span class=\"code-snippet_outer\">metadata(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">## paths<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- splatSimulate(de.prob = 0.2, nGenes = 1000, method = \"paths\",<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- logNormCounts(sim.paths)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- runPCA(sim.paths)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.paths, colour_by = \"Step\")<\/span><\/code><code><span class=\"code-snippet_outer\">colData(sim.paths)$Step<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">## batches<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- splatSimulate(batchCells = c(50, 50), verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- logNormCounts(sim.batches)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- runPCA(sim.batches)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.batches, colour_by = \"Batch\")<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.batches)$BatchFacBatch1<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.batches)$BatchFacBatch2<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6700\u540epca\u53ef\u89c6\u5316\u7684\u7ed3\u679c\u5982\u4e0b\uff1a<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9851632047477745\" data-type=\"png\" data-w=\"674\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_TBskmFcZpvDk3GWasYlXuNRQjq9BFw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtQkzLcGKeQ8PTB1Dy62kiaicbUTTBskmFcZpvDk3GWasYlXuNRQjq9BFw\/640?wx_fmt=png'\" \/><\/p>\n<p><span style=\"font-size: 14px;\">\u901a\u8fc7\u5b66\u4e60\u8fd9\u4e9b\u4ee3\u7801\uff0c\u4f60\u53ef\u4ee5\u4e86\u89e3\u5982\u4f55\u4f7f\u7528splatter\u548cscater\u5305\u8fdb\u884c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u7684\u6a21\u62df\u548c\u5206\u6790\uff0c\u5305\u62ec\u6a21\u62df\u6570\u636e\u7684\u5feb\u901f\u751f\u6210\u3001\u53c2\u6570\u4f30\u8ba1\u3001\u81ea\u5b9a\u4e49\u53c2\u6570\u521b\u5efa\u3001\u6570\u636e\u63d0\u53d6\u3001\u6570\u636e\u6807\u51c6\u5316\u548c\u964d\u7ef4\u5904\u7406\u7b49\u3002\u600e\u4e48\u6837\uff0c\u662f\u4e0d\u662f\u5f88\u7b80\u5355\uff0c\u4f60\u5b66\u5e9f\u4e86\u561b\uff01\uff1f<\/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\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491705&idx=1&sn=9ff9b6da28b3a256a99c6697d589be66&chksm=cf7f70bcf808f9aafd1019a0bba3dd3a55e2867dbb9a09203f13c2683adf867094637c405ed1&scene=21#wechat_redirect\" textvalue=\"2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86<\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" 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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\",\"time\":\"2023-10-16 19:00:07\",\"timeStamp\":\"1697454007\"};\n<\/script><br \/>\n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247494145&idx=1&sn=51aba9b01df3ef447db55c5ac4f6d48b&chksm=cf7f7ac4f808f3d27e70d9234fc0485898d3c041300056b25db28263a4d95fd594037e25e381#rd\" target=\"_blank\" rel=\"noopener\">\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span id=\"copyright_logo\" class=\"wx_tap_link js_wx_tap_highlight rich_media_meta icon_appmsg_tag appmsg_title_tag weui-wa-hotarea\">\u539f\u521b <\/span><span class=\"rich_media_meta 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\">2023-10-16 19:00:07<\/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=3142533467331887107#wechat_redirect\" title=\"\u5355\u7ec6\u80de\u6d4b\u5e8f\" target=\"_blank\" rel=\"noopener\">#\u5355\u7ec6\u80de\u6d4b\u5e8f<\/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><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 data-mpa-powered-by=\"yiban.io\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">hello\uff0c\u4f60\u77e5\u9053\u6709\u4e00\u4e2aR\u5305\u53ef\u4ee5\u751f\u6210\u6a21\u62df\u5355\u7ec6\u80deRNA-seq\u7684\u6570\u636e\uff0c\u5e76\u53ef\u4ee5\u7528\u4e8e\u8bc4\u4f30\u548c\u6bd4\u8f83\u4e0d\u540c\u7684\u5206\u6790\u65b9\u6cd5\u561b\uff1f\u4eca\u5929\u5c0f\u679c\u5c31\u6765\u6559\u5927\u5bb6\u5982\u4f55\u4f7f\u7528\u8fd9\u4e2aR\u5305\uff0c\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u770b\u4e0b\u53bb\u5427\uff01<\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u4e86\u89e3splatter<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"font-size: 14px;letter-spacing: 0.034em;\">splatter\u662f\u4e00\u4e2a\u7528\u4e8e\u6a21\u62df\u548c\u5206\u6790\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\u7684R\u8bed\u8a00\u5305\u3002\u5b83\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u529f\u80fd\uff0c\u4f7f\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u751f\u6210\u6a21\u62df\u6570\u636e\u3001\u8fdb\u884c\u53c2\u6570\u4f30\u8ba1\u3001\u6570\u636e\u6807\u51c6\u5316\u3001\u964d\u7ef4\u5206\u6790\u7b49\u3002\u4e0b\u9762\u5c0f\u679c\u6765\u4ecb\u7ecd\u4e00\u4e0bsplatter\u5305\u7684\u4e3b\u8981\u529f\u80fd\u548c\u4f5c\u7528\uff1a<br \/><\/span><\/p>\n<ol class=\"list-paddingleft-1\">\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\"><strong>\u6a21\u62df\u6570\u636e\u751f\u6210\uff1a<\/strong>splatter\u5141\u8bb8\u7528\u6237\u6839\u636e\u81ea\u5b9a\u4e49\u7684\u53c2\u6570\u751f\u6210\u6a21\u62df\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\"><strong>\u53c2\u6570\u4f30\u8ba1\uff1a<\/strong>splatter\u63d0\u4f9b\u4e86\u529f\u80fd\u5f3a\u5927\u7684\u53c2\u6570\u4f30\u8ba1\u65b9\u6cd5\uff0c\u53ef\u4ee5\u4ece\u7ed9\u5b9a\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u4e2d\u4f30\u8ba1\u51fa\u6a21\u578b\u7684\u53c2\u6570\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\"><strong>\u6570\u636e\u6807\u51c6\u5316\uff1a<\/strong>splatter\u5305\u542b\u4e86\u4e00\u7cfb\u5217\u6570\u636e\u6807\u51c6\u5316\u65b9\u6cd5\uff0c\u5982\u5bf9\u6570\u8f6c\u6362\u3001\u5f52\u4e00\u5316\u7b49\uff0c\u53ef\u4ee5\u5e2e\u52a9\u7528\u6237\u5bf9\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u9884\u5904\u7406\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\"><strong>\u964d\u7ef4\u5206\u6790\uff1a<\/strong>splatter\u652f\u6301\u5e38\u7528\u7684\u964d\u7ef4\u5206\u6790\u65b9\u6cd5\uff0c\u5982\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\uff0c\u53ef\u4ee5\u5c06\u9ad8\u7ef4\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u6295\u5f71\u5230\u4e8c\u7ef4\u6216\u4e09\u7ef4\u7a7a\u95f4\u4e2d\uff0c\u65b9\u4fbf\u53ef\u89c6\u5316\u548c\u8fdb\u4e00\u6b65\u7684\u6570\u636e\u89e3\u91ca\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\"><strong>\u6570\u636e\u53ef\u89c6\u5316\uff1a<\/strong>splatter\u63d0\u4f9b\u4e86\u591a\u79cd\u7ed8\u56fe\u51fd\u6570\uff0c\u7528\u4e8e\u53ef\u89c6\u5316\u6a21\u62df\u6570\u636e\u3001\u53c2\u6570\u4f30\u8ba1\u7ed3\u679c\u3001\u6807\u51c6\u5316\u540e\u7684\u6570\u636e\u3001\u964d\u7ef4\u5206\u6790\u7ed3\u679c\u7b49\u3002<\/span><\/p>\n<\/li>\n<\/ol>\n<p><span style=\"font-size: 14px;\">\u603b\u800c\u8a00\u4e4b\uff0csplatter\u662f\u4e00\u4e2a\u529f\u80fd\u4e30\u5bcc\u7684R\u5305\uff0c\u901a\u8fc7\u6a21\u62df\u751f\u6210\u3001\u53c2\u6570\u4f30\u8ba1\u3001\u6570\u636e\u6807\u51c6\u5316\u548c\u964d\u7ef4\u5206\u6790\u7b49\u529f\u80fd\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u66f4\u597d\u5730\u7406\u89e3\u548c\u5206\u6790\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\uff0c\u4e3a\u5355\u7ec6\u80de\u7814\u7a76\u63d0\u4f9b\u4e86\u6709\u529b\u7684\u5de5\u5177\u548c\u65b9\u6cd5\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u63a5\u4e0b\u6765\u5c0f\u679c\u5c06\u4f7f\u7528R\u8bed\u8a00\u4e2d\u7684splatter\u548cscater\u5305\u8fdb\u884c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u6a21\u62df\u548c\u5206\u6790\u3002\u90a3\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u5b66\u8d77\u6765\u5427\uff01<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3888888888888889\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"1080\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-16_\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\/1_IlmBAWe69EMUPMhNEgrv6NXX85lJxg.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwyrj7kbUR3ULG9ZUbLrLkgibzL8qUpQROfe8ebc3gNSnu1dIlmBAWe69EMUPMhNEgrv6NXX85lJxg\/640?wx_fmt=jpeg'\" \/><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">1. \u5feb\u901f\u521b\u5efa\u6a21\u62df\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u9996\u5148\u6211\u4eec\u4f7f\u7528splatter\u5305\u4e2d\u7684mockSCE\u51fd\u6570\u5feb\u901f\u521b\u5efa\u4e00\u4e2a\u6a21\u62df\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u3002mockSCE\u51fd\u6570\u53ef\u4ee5\u8bbe\u7f6e\u7ec6\u80de\u7684\u6570\u91cf\uff08ncells\uff09\u3001\u57fa\u56e0\u7684\u6570\u91cf\uff08ngenes\uff09\u548cspike-in\u7684\u6570\u91cf\uff08nspikes\uff09\uff0c\u5e76\u8fd4\u56de\u4e00\u4e2aSingleCellExperiment\uff08SCE\uff09\u5bf9\u8c61\u3002\u4ee3\u7801\u4e2d\u7684set.seed(1)\u7528\u4e8e\u8bbe\u7f6e\u968f\u673a\u6570\u79cd\u5b50\uff0c\u4fdd\u8bc1\u7ed3\u679c\u7684\u53ef\u91cd\u590d\u6027\u3002\u6700\u540e\uff0c\u6211\u4eec\u4f7f\u7528counts\u51fd\u6570\u67e5\u770b\u6a21\u62df\u6570\u636e\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u3002<\/span><br \/><\/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=\"cs\"><code><span class=\"code-snippet_outer\">library(splatter)<\/span><\/code><code><span class=\"code-snippet_outer\">library(scater)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">### 1. \u5feb\u901f\u521b\u5efa\u6a21\u62df\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\"># Usage<\/span><\/code><code><span class=\"code-snippet_outer\"># mockSCE(ncells = 200, ngenes = 2000, nspikes = 100)<\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(1)<\/span><\/code><code><span class=\"code-snippet_outer\">sce <- mockSCE() # class: SingleCellExperiment<\/span><\/code><code><span class=\"code-snippet_outer\">counts(sce)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u6a21\u62df\u751f\u6210\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff1a<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6253602305475504\" data-type=\"png\" data-w=\"1041\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-16_\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\/2_bSyY6vTZzMrIXefO6fedHjh4XzdjMA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtdVZ2CHfs2jHEP3GxxrKRBon3bSyY6vTZzMrIXefO6fedHjh4XzdjMA\/640?wx_fmt=png'\" \/><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">2. \u53c2\u6570\u4f30\u8ba1<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u4f7f\u7528splatEstimate\u51fd\u6570\u4ece\u7ed9\u5b9a\u7684\u6570\u636e\u4e2d\uff08\u8fd9\u91cc\u662f\u4e0a\u4e00\u90e8\u5206\u6a21\u62df\u751f\u6210\u7684\u6570\u636e\uff09\u4f30\u8ba1\u53c2\u6570\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\">### 2. \u53c2\u6570\u4f30\u8ba1<\/span><\/code><code><span class=\"code-snippet_outer\"># \u4ece\u6570\u636e\uff08\u6a21\u62df\u6570\u636e\u6216\u771f\u5b9e\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff09\u4e2d\u4f30\u8ba1\u53c2\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">params <- splatEstimate(sce) # Params object<\/span><\/code><\/pre>\n<\/section>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">3. \u81ea\u5b9a\u4e49\u53c2\u6570\uff0c\u521b\u5efa\u6a21\u62df\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u6765\u5b66\u4e60\u5982\u4f55\u6839\u636e\u81ea\u5b9a\u4e49\u53c2\u6570\u521b\u5efa\u6a21\u62df\u6570\u636e\u3002\u9996\u5148\uff0c\u4f7f\u7528newSplatParams\u51fd\u6570\u521b\u5efa\u4e00\u4e2a\u53c2\u6570\u5bf9\u8c61params\u3002\u7136\u540e\uff0c\u4f7f\u7528getParam\u51fd\u6570\u67e5\u770b\u53c2\u6570\u5bf9\u8c61\u4e2d\u7684\u53c2\u6570\u8bbe\u5b9a\u3002\u63a5\u4e0b\u6765\uff0c\u4f7f\u7528setParam\u548csetParams\u51fd\u6570\u8bbe\u7f6e\u53c2\u6570\u5bf9\u8c61\u4e2d\u7684\u53c2\u6570\u3002\u6700\u540e\uff0c\u4f7f\u7528splatSimulate\u51fd\u6570\u6839\u636e\u53c2\u6570\u5bf9\u8c61\u521b\u5efa\u6a21\u62df\u6570\u636e\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<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\">### 3. \u81ea\u5b9a\u4e49\u53c2\u6570\uff0c\u521b\u5efa\u6a21\u62df\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\"># \u521b\u5efa\u53c2\u6570\u5bf9\u8c61<\/span><\/code><code><span class=\"code-snippet_outer\">params <- newSplatParams() #\u9ed8\u8ba410000 Genes\uff0c100 Cells<\/span><\/code><code><span class=\"code-snippet_outer\"># \u67e5\u770b\u53c2\u6570\u5bf9\u8c61\u4e2d\u7684\u53c2\u6570\u8bbe\u5b9a<\/span><\/code><code><span class=\"code-snippet_outer\">getParam(params, \"nGenes\")<\/span><\/code><code><span class=\"code-snippet_outer\">getParam(params, \"nCells\")<\/span><\/code><code><span class=\"code-snippet_outer\">getParams(params, c(\"nGenes\", \"mean.rate\", \"mean.shape\"))<\/span><\/code><code><span class=\"code-snippet_outer\"># \u8bbe\u5b9a\u53c2\u6570\u5bf9\u8c61\u4e2d\u7684\u53c2\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParam(params, \"nGenes\", 5000)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParam(params, \"batchCells\", 50)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParams(params, mean.shape = 0.5, de.prob = 0.2)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParams(params, update = list(nGenes = 8000, mean.rate = 0.5))<\/span><\/code><\/pre>\n<\/section>\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=\"cs\"><code><span class=\"code-snippet_outer\"># \u6839\u636e\u53c2\u6570\uff0c\u521b\u5efa\u6a21\u62df\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">sim <- splatSimulate(params)<\/span><\/code><\/pre>\n<\/section>\n<p><strong><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.4609375\" data-type=\"png\" data-w=\"640\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_FMptqBicqugS405mtOSrSIdXJImiag.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtbd2Ct3ibLVHJF4rOSSSpsyib4tXcFMptqBicqugS405mtOSrSIdXJImiag\/640?wx_fmt=png'\" \/><\/strong><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">4. \u63d0\u53d6SingleCellExperiment\u7c7b\u4fe1\u606f<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4ecb\u7ecd\u63d0\u53d6SingleCellExperiment\u5bf9\u8c61\u4e2d\u7684\u4fe1\u606f\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<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=\"objectivec\"><code><span class=\"code-snippet_outer\">### 4. \u63d0\u53d6SingleCellExperiment\u7c7b\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">class(sim)<\/span><\/code><code><span class=\"code-snippet_outer\"># Information about genes<\/span><\/code><code><span class=\"code-snippet_outer\">head(rowData(sim))<\/span><\/code><code><span class=\"code-snippet_outer\"># Information about cells<\/span><\/code><code><span class=\"code-snippet_outer\">head(colData(sim))<\/span><\/code><code><span class=\"code-snippet_outer\"># Gene by cell matrices<\/span><\/code><code><span class=\"code-snippet_outer\">names(assays(sim))<\/span><\/code><code><span class=\"code-snippet_outer\"># Example of cell means matrix<\/span><\/code><code><span class=\"code-snippet_outer\">assays(sim)$CellMeans[1:5, 1:5]<\/span><\/code><code><span class=\"code-snippet_outer\"># \u8868\u8fbe\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">counts <- counts(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">counts[1:3,1:5]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">class(counts) # \"matrix\" \"array\" <\/span><\/code><code><span class=\"code-snippet_outer\">typeof(counts) # [1] \"integer\"<\/span><\/code><code><span class=\"code-snippet_outer\">dim(counts) #[1] 8000 100<\/span><\/code><\/pre>\n<\/section>\n<p><strong>\u8fd0\u884c\u7ed3\u679c\u5982\u4e0b\uff1a<\/strong><\/p>\n<p><strong><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5316804407713499\" data-type=\"png\" data-w=\"363\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_e65e7lGGgws54ibhIGiacLSGUOIuGA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtrj0GLxxNLXMNRULCEg24VYHSqqe65e7lGGgws54ibhIGiacLSGUOIuGA\/640?wx_fmt=png'\" \/><\/strong><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">5. \u6570\u636e\u6807\u51c6\u5316\uff0c\u5bf9\u6570\u5316\u548c\u964d\u7ef4<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8fdb\u4e00\u6b65\u5730\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u5982\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316\u3001\u5bf9\u6570\u5316\u548c\u964d\u7ef4\u5904\u7406\u3002\u9996\u5148\uff0c\u4f7f\u7528logNormCounts\u51fd\u6570\u5bf9SingleCellExperiment\u5bf9\u8c61\u4e2d\u7684counts\u503c\u8fdb\u884c\u5bf9\u6570\u8f6c\u6362\u548c\u5f52\u4e00\u5316\u3002\u901a\u8fc7logcounts\u51fd\u6570\u53ef\u4ee5\u67e5\u770b\u8f6c\u6362\u540e\u7684\u5bf9\u6570\u8868\u8fbe\u77e9\u9635\u3002\u7136\u540e\uff0c\u4f7f\u7528runPCA\u51fd\u6570\u5bf9\u6570\u636e\u8fdb\u884cPCA\u964d\u7ef4\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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">### 5. \u6570\u636e\u6807\u51c6\u5316\uff0c\u5bf9\u6570\u5316\u548c\u964d\u7ef4<\/span><\/code><code><span class=\"code-snippet_outer\">## {scuttle}\u5305\u7684\u51fd\u6570:logNormCounts<\/span><\/code><code><span class=\"code-snippet_outer\">## {scater}\u5305\u7684\u51fd\u6570:runPCA,plotPCA<\/span><\/code><code><span class=\"code-snippet_outer\"># SingleCellExperiment \u5bf9\u8c61\u7684counts\u503c\u8ba1\u7b97\u5bf9\u6570\u8f6c\u6362\u7684\u5f52\u4e00\u5316\u8868\u8fbe\u5f0f\u503c<\/span><\/code><code><span class=\"code-snippet_outer\">sim <- logNormCounts(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">counts(sim)[1:3,1:5]<\/span><\/code><code><span class=\"code-snippet_outer\">logcounts(sim)[1:3,1:5]<\/span><\/code><code><span class=\"code-snippet_outer\"># PCA\u964d\u7ef4<\/span><\/code><code><span class=\"code-snippet_outer\">sim <- runPCA(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6700\u540e\uff0c\u5c0f\u679c\u4f7f\u7528plotPCA\u51fd\u6570\u7ed8\u5236PCA\u964d\u7ef4\u7ed3\u679c\u3002\u6211\u4eec\u6765\u770b\u770b\u53ef\u89c6\u5316\u7684\u7ed3\u679c\u662f\u4ec0\u4e48\u6837\u5427\uff01<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9933598937583001\" data-type=\"png\" data-w=\"753\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_hE9PvQ2gr8LWsrWDzZhJhe0lmo8l0w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtrqicXPVibjHRh359yGGrxVldhhhE9PvQ2gr8LWsrWDzZhJhe0lmo8l0w\/640?wx_fmt=png'\" \/><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">6. \u521b\u5efa\u590d\u6742\u7684\u6a21\u62df\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u6700\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u521b\u5efa\u66f4\u590d\u6742\u7684\u6a21\u62df\u6570\u636e\uff0c\u5305\u62ec\u5177\u6709\u7ec4\u7ed3\u6784\u3001\u8def\u5f84\u7ed3\u6784\u548c\u6279\u6b21\u6548\u5e94\u7684\u6a21\u62df\u6570\u636e\u3002<\/span><br \/><\/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=\"cs\"><code><span class=\"code-snippet_outer\">### 6. \u521b\u5efa\u590d\u6742\u7684\u6a21\u62df\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">## groups<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- splatSimulate(group.prob = c(0.3, 0.7), method = \"groups\",<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- logNormCounts(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- runPCA(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.groups, colour_by = \"Group\")<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u6765\u770b\u770b\u964d\u7ef4\u540e\u7684\u7ed3\u679c\uff1a<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0026702269692924\" data-type=\"png\" data-w=\"749\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-16_\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\/6_u58ksB6zLNmrXWOfb7Q25GrFHgKhQg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtblCI54RiaZgHXbnQ063S3xgX5u58ksB6zLNmrXWOfb7Q25GrFHgKhQg\/640?wx_fmt=png'\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">dim(counts(sim.groups))<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.groups)$DEFacGroup1<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.groups)$DEFacGroup2<\/span><\/code><code><span class=\"code-snippet_outer\">metadata(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">## paths<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- splatSimulate(de.prob = 0.2, nGenes = 1000, method = \"paths\",<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- logNormCounts(sim.paths)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- runPCA(sim.paths)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.paths, colour_by = \"Step\")<\/span><\/code><code><span class=\"code-snippet_outer\">colData(sim.paths)$Step<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">## batches<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- splatSimulate(batchCells = c(50, 50), verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- logNormCounts(sim.batches)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- runPCA(sim.batches)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.batches, colour_by = \"Batch\")<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.batches)$BatchFacBatch1<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.batches)$BatchFacBatch2<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6700\u540epca\u53ef\u89c6\u5316\u7684\u7ed3\u679c\u5982\u4e0b\uff1a<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9851632047477745\" data-type=\"png\" data-w=\"674\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_TBskmFcZpvDk3GWasYlXuNRQjq9BFw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxa9pofo46oAUBa6qvibwQRtQkzLcGKeQ8PTB1Dy62kiaicbUTTBskmFcZpvDk3GWasYlXuNRQjq9BFw\/640?wx_fmt=png'\" \/><\/p>\n<p><span style=\"font-size: 14px;\">\u901a\u8fc7\u5b66\u4e60\u8fd9\u4e9b\u4ee3\u7801\uff0c\u4f60\u53ef\u4ee5\u4e86\u89e3\u5982\u4f55\u4f7f\u7528splatter\u548cscater\u5305\u8fdb\u884c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u7684\u6a21\u62df\u548c\u5206\u6790\uff0c\u5305\u62ec\u6a21\u62df\u6570\u636e\u7684\u5feb\u901f\u751f\u6210\u3001\u53c2\u6570\u4f30\u8ba1\u3001\u81ea\u5b9a\u4e49\u53c2\u6570\u521b\u5efa\u3001\u6570\u636e\u63d0\u53d6\u3001\u6570\u636e\u6807\u51c6\u5316\u548c\u964d\u7ef4\u5904\u7406\u7b49\u3002\u600e\u4e48\u6837\uff0c\u662f\u4e0d\u662f\u5f88\u7b80\u5355\uff0c\u4f60\u5b66\u5e9f\u4e86\u561b\uff01\uff1f<\/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\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491705&idx=1&sn=9ff9b6da28b3a256a99c6697d589be66&chksm=cf7f70bcf808f9aafd1019a0bba3dd3a55e2867dbb9a09203f13c2683adf867094637c405ed1&scene=21#wechat_redirect\" textvalue=\"2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86<\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491909&idx=1&sn=902e34bcf53e605fba2b457ec6a33e36&chksm=cf7f7180f808f8961542f458a49da14e85d8831449fb65fbf2623d55affc564686a5422f56fd&scene=21#wechat_redirect\" textvalue=\"3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8<\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491905&idx=1&sn=fb34ebd6282962c7803badaee7a39096&chksm=cf7f7184f808f8929608c0050344ad86193d0fc6455c1c18e16cc17bf4b37832b63d3b18284e&scene=21#wechat_redirect\" textvalue=\"4.\u5c0f\u679c\u5e26\u4f60\u7ed8\u5236ROC\u66f2\u7ebf\u8bc4\u4f30\u751f\u5b58\u9884\u6d4b\u80fd\u529b\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\"><span style=\"font-size: 14px;\">4.\u5c0f\u679c\u5e26\u4f60\u7ed8\u5236ROC\u66f2\u7ebf\u8bc4\u4f30\u751f\u5b58\u9884\u6d4b\u80fd\u529b<\/span><\/a><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;text-align: left;\"><span style=\"font-size: 10.5pt;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493633&idx=1&sn=2263dfe7572c0bcf6816c2c1a37d79de&chksm=cf7f78c4f808f1d2209321d6ace39fde5fa60c0691b56f88eac21916f5a2872ce8ee345f1d5f&scene=21#wechat_redirect\" textvalue=\"\u4f60\u5df2\u9009\u4e2d\u4e86\u6dfb\u52a0\u94fe\u63a5\u7684\u5185\u5bb9\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.4255555555555556\" data-w=\"900\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-16_\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\/8_3enDMf2LD6pjia3zQolKXIfTwuh6AA.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxweqRKIWbRUBSWSGID9aog3q3QVgsHZplb1JyboXh8CPz6b3enDMf2LD6pjia3zQolKXIfTwuh6AA\/640?wx_fmt=jpeg&wxfrom=5&wx_lazy=1&wx_co=1'\" \/><\/span><\/a><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3888888888888889\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"1080\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-16_\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\/9_SibFRUHIk0cCbShYgOsGDPrxeHkEtw.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwyrj7kbUR3ULG9ZUbLrLkgvrEB1jg0GibYczZiaOORjzpxpIjSibFRUHIk0cCbShYgOsGDPrxeHkEtw\/640?wx_fmt=jpeg'\" \/><\/p>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01 \u539f\u521b \u5c0f\u679c […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","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\/54807"}],"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=54807"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/54807\/revisions"}],"predecessor-version":[{"id":54817,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/54807\/revisions\/54817"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=54807"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=54807"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=54807"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}