{"id":61253,"date":"2024-10-28T14:53:22","date_gmt":"2024-10-28T06:53:22","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61253"},"modified":"2024-10-28T14:53:22","modified_gmt":"2024-10-28T06:53:22","slug":"%e5%8d%95%e7%bb%86%e8%83%9erna%e6%b5%8b%e5%ba%8f%e6%a8%a1%e6%8b%9f%ef%bc%8csplatter%e5%8c%85%e8%ae%a9%e4%bd%a0%e7%9a%84%e7%a0%94%e7%a9%b6%e9%a3%9e%e8%b5%b7%e6%9d%a5%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61253","title":{"rendered":"\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6a21\u62df\uff0cSplatter\u5305\u8ba9\u4f60\u7684\u7814\u7a76\u98de\u8d77\u6765\uff01"},"content":{"rendered":"\n<p><\/p>\n\n\n\n<p>\u563f\uff0c\u79d1\u7814\u5c0f\u4f19\u4f34\u4eec\uff0c\u5c0f\u5e08\u59b9\u6211\u53c8\u6765\u5566\uff01\u4eca\u5929\uff0c\u6211\u8981\u7ed9\u5927\u5bb6\u5e26\u6765\u4e00\u4e2a\u8d85\u7ea7\u5b9e\u7528\u7684\u751f\u7269\u4fe1\u606f\u5b66\u5de5\u5177\u2014\u2014Splatter\u5305\u3002\u5728\u8fd9\u4e2a\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6570\u636e\u7206\u70b8\u7684\u65f6\u4ee3\uff0c\u4f60\u662f\u4e0d\u662f\u4e5f\u5728\u4e3a\u5982\u4f55\u83b7\u53d6\u548c\u5904\u7406\u8fd9\u4e9b\u590d\u6742\u7684\u6570\u636e\u800c\u5934\u75bc\uff1f\u522b\u62c5\u5fc3\uff0c\u6709\u4e86Splatter\u5305\uff0c\u6211\u4eec\u53ef\u4ee5\u8f7b\u677e\u6a21\u62df\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6570\u636e\uff0c\u8ba9\u6570\u636e\u5206\u6790\u53d8\u5f97\u66f4\u52a0\u7b80\u5355\u76f4\u89c2\u3002<\/p>\n\n\n\n<p>Splatter\u662f\u4e00\u4e2aR\u5305\uff0c\u4e13\u95e8\u7528\u4e8e\u7b80\u5355\u6a21\u62df\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6570\u636e\u3002\u8fd9\u4e2a\u5305\u7684\u529f\u80fd\u975e\u5e38\u5f3a\u5927\uff0c\u5b83\u4e0d\u4ec5\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u7406\u89e3\u6570\u636e\u7684\u7279\u6027\uff0c\u8fd8\u80fd\u8ba9\u6211\u4eec\u5728\u5b9e\u9645\u7814\u7a76\u4e2d\u66f4\u52a0\u5f97\u5fc3\u5e94\u624b\u3002\u901a\u8fc7\u8fd9\u4e2a\u5305\uff0c\u6211\u4eec\u53ef\u4ee5\u6a21\u62df\u51fa\u4e0e\u771f\u5b9e\u6570\u636e\u6781\u4e3a\u76f8\u4f3c\u7684\u5355\u7ec6\u80de\u6570\u636e\u96c6\uff0c\u8fd9\u5bf9\u4e8e\u9a8c\u8bc1\u5206\u6790\u65b9\u6cd5\u3001\u6d4b\u8bd5\u65b0\u7684\u7b97\u6cd5\u6216\u8fdb\u884c\u6559\u5b66\u6f14\u793a\u90fd\u662f\u975e\u5e38\u6709\u7528\u7684\u3002<\/p>\n\n\n\n<p>\u5728\u8fd9\u4e2a\u6559\u7a0b\u4e2d\uff0c\u5c0f\u5e08\u59b9\u5c06\u5e26\u4f60\u4e00\u6b65\u6b65\u4e86\u89e3Splatter\u5305\u7684\u5b89\u88c5\u3001\u5feb\u901f\u5165\u95e8\u6307\u5357\uff0c\u4ee5\u53ca\u5982\u4f55\u8fdb\u884c\u53c2\u6570\u4f30\u8ba1\u548c\u6570\u636e\u6a21\u62df\u3002<strong>\u6ce8\u610f\u54e6\uff0c\u8fd9\u4e2a<\/strong><strong>R\u5305\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668<\/strong><strong>\u54e6<\/strong><strong>\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u5e08\u59b9\u79df\u8d41\u6027\u4ef7\u6bd4\u9ad8\u7684\u670d\u52a1\u5668<\/strong><strong>~ <\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u51c6\u5907\u597d\u4e86\u5417\uff1f\u8ba9\u6211\u4eec\u4e00\u8d77\u5f00\u542f\u8fd9\u573a\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u7684\u5947\u5999\u4e4b\u65c5\u5427\uff01<strong>\u5982\u679c\u5728\u65c5\u9014\u4e2d\u9047\u5230\u4efb\u4f55\u95ee\u9898\uff0c\u8bb0\u5f97\u627e\u5c0f\u5e08\u59b9\u5e2e\u5fd9\u54e6\uff01<\/strong><\/p>\n\n\n\n<p>\u9996\u5148\uff0c\u8ba9\u6211\u4eec\u5f00\u59cb\u5b89\u88c5multistateQTL\u5305\u548c\u53e6\u5916\u9700\u8981\u7528\u5230\u7684\u5305\uff1a<\/p>\n\n\n\n<p>if (!require(&#8220;BiocManager&#8221;, quietly=TRUE))<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;install.packages(&#8220;BiocManager&#8221;)<\/p>\n\n\n\n<p>BiocManager::install(&#8220;splatter&#8221;)<\/p>\n\n\n\n<p>BiocManager::install(&#8220;scater&#8221;)<\/p>\n\n\n\n<p>\u5b89\u88c5\u597d\u4e86\u4e4b\u540e\uff0c\u8bb0\u5f97\u52a0\u8f7d\u8fd9\u4e9b\u5fc5\u8981\u7684\u5e93\uff1a<\/p>\n\n\n\n<p>lsuppressPackageStartupMessages({<\/p>\n\n\n\n<p>&nbsp;&nbsp;library(splatter)<\/p>\n\n\n\n<p>&nbsp;&nbsp;library(scater)<\/p>\n\n\n\n<p>})<\/p>\n\n\n\n<p><strong>\u4e00\u3001<\/strong><strong>\u5feb\u901f\u4e0a\u624b Splatter\u5305<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u5982\u679c\u4f60\u5df2\u7ecf\u6709\u4e86\u4e00\u4e2a\u7c7b\u4f3c\u4e8e\u4f60\u60f3\u8981\u6a21\u62df\u7684\u8ba1\u6570\u6570\u636e\u96c6\uff0c\u90a3\u4e48\u53ea\u9700\u8981\u4e24\u6b65\uff0c\u6211\u4eec\u5c31\u80fd\u521b\u5efa\u4e00\u4e2a\u6a21\u62df\u7684\u6570\u636e\u96c6\u3002\u4e0b\u9762\u662f\u5982\u4f55\u7528`scater`\u5305\u751f\u6210\u4e00\u4e2a\u6a21\u62df\u6570\u636e\u96c6\u7684\u4f8b\u5b50\uff1a<\/p>\n\n\n\n<p># \u521b\u5efa\u6a21\u62df\u6570\u636e<\/p>\n\n\n\n<p>set.seed(1)<\/p>\n\n\n\n<p>sce &lt;- mockSCE()<\/p>\n\n\n\n<p># \u4ece\u6a21\u62df\u6570\u636e\u4f30\u8ba1\u53c2\u6570<\/p>\n\n\n\n<p>params &lt;- splatEstimate(sce)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"18\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097040893_15832A4C-FA40-4ba0-94CB-D37A7D305108.png?resize=554%2C18\" alt=\"\" class=\"wp-image-61254\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097040893_15832A4C-FA40-4ba0-94CB-D37A7D305108.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097040893_15832A4C-FA40-4ba0-94CB-D37A7D305108.png?resize=300%2C10 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u8fd9\u4e00\u6b65\uff0cSplatter\u4f1a\u63d0\u9192\u6211\u4eec\uff0c\u5b83\u53d1\u73b0\u5e93\u5927\u5c0f\u662f\u6b63\u6001\u5206\u5e03\u800c\u4e0d\u662f\u5bf9\u6570\u6b63\u6001\u5206\u5e03\u3002\u8fd9\u4e2a\u63d0\u793a\u5f88\u6709\u7528\uff0c\u56e0\u4e3a\u5b83\u544a\u8bc9\u6211\u4eec\u6570\u636e\u7684\u5206\u5e03\u7279\u6027\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u8fd9\u4e2a\u4fe1\u606f\u8c03\u6574\u6a21\u62df\u53c2\u6570\u3002<\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u7528\u4f30\u8ba1\u51fa\u7684\u53c2\u6570\u6765\u6a21\u62df\u65b0\u7684\u6570\u636e\u96c6\uff1a<\/p>\n\n\n\n<p># \u4f7f\u7528\u4f30\u8ba1\u7684\u53c2\u6570\u6a21\u62df\u6570\u636e<\/p>\n\n\n\n<p>sim &lt;- splatSimulate(params)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"336\" height=\"167\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097050616_3007AACF-5579-4342-8AF1-99CDA4EA4EAA.png?resize=336%2C167\" alt=\"\" class=\"wp-image-61255\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097050616_3007AACF-5579-4342-8AF1-99CDA4EA4EAA.png?w=336 336w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097050616_3007AACF-5579-4342-8AF1-99CDA4EA4EAA.png?resize=300%2C149 300w\" sizes=\"(max-width: 336px) 100vw, 336px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5728\u6a21\u62df\u8fc7\u7a0b\u4e2d\uff0cSplatter\u4f1a\u6267\u884c\u4e00\u7cfb\u5217\u6b65\u9aa4\uff1a\u83b7\u53d6\u53c2\u6570\u3001\u521b\u5efa\u6a21\u62df\u5bf9\u8c61\u3001\u6a21\u62df\u5e93\u5927\u5c0f\u3001\u57fa\u56e0\u5747\u503c\u3001\u751f\u7269\u5b66\u53d8\u5f02\u7cfb\u6570\uff08BCV\uff09\u3001\u8ba1\u6570\u3001\u5982\u679c\u9700\u8981\u7684\u8bdd\u6a21\u62dfdropout\uff08\u6570\u636e\u4e22\u5931\uff09\uff0c\u4ee5\u53ca\u5c06\u7ed3\u679c\u7a00\u758f\u5316\u3002\u8fd9\u4e2a\u8fc7\u7a0b\u4f1a\u751f\u6210\u4e00\u4e2a\u7a00\u758f\u77e9\u9635\uff0c\u8fd9\u6709\u52a9\u4e8e\u6211\u4eec\u66f4\u6709\u6548\u5730\u5904\u7406\u548c\u5206\u6790\u6570\u636e\u3002<\/p>\n\n\n\n<p>\u7b80\u5355\u6765\u8bf4\uff0c\u6211\u4eec\u9996\u5148\u4ece\u4e00\u4e2a\u6570\u636e\u96c6\u4e2d\u4f30\u8ba1\u51fa\u6a21\u62df\u6240\u9700\u7684\u53c2\u6570\uff0c\u7136\u540e\u7528\u8fd9\u4e9b\u53c2\u6570\u6765\u521b\u5efa\u4e00\u4e2a\u65b0\u7684\u6a21\u62df\u6570\u636e\u96c6\u3002\u63a5\u4e0b\u6765\u7684\u90e8\u5206\u4f1a\u8be6\u7ec6\u89e3\u91ca\u8fd9\u4e9b\u6b65\u9aa4\uff0c\u4f46\u73b0\u5728\uff0c\u6211\u4eec\u53ea\u9700\u8981\u77e5\u9053\u8fd9\u4e24\u4e2a\u4e3b\u8981\u6b65\u9aa4\u5c31\u53ef\u4ee5\u4e86\u3002<\/p>\n\n\n\n<p><strong>\u4e8c\u3001<\/strong><strong>Splat\u6a21\u62df\uff1a\u6570\u636e\u751f\u6210\u7684\u5965\u79d8<\/strong><\/p>\n\n\n\n<p>\u5c0f\u4f19\u4f34\u4eec\uff0c\u5728\u6df1\u5165\u7814\u7a76\u53c2\u6570\u4f30\u7b97\u4e4b\u524d\uff0c\u5148\u8ddf\u5c0f\u5e08\u59b9\u5feb\u901f\u4e86\u89e3\u4e00\u4e0bSplatter\u5305\u7684Splat\u6a21\u62df\u662f\u600e\u4e48\u56de\u4e8b\u3002Splat\u5176\u5b9e\u5c31\u662fSplatter\u5305\u91cc\u7528\u6765\u751f\u6210\u6a21\u62df\u6570\u636e\u7684\u6a21\u578b\u3002\u5b83\u7528\u4f3d\u9a6c-\u6cca\u677e\u5206\u5e03\u6765\u6a21\u62df\u6bcf\u4e2a\u57fa\u56e0\u5728\u6bcf\u4e2a\u7ec6\u80de\u4e2d\u7684\u8868\u8fbe\u8ba1\u6570\u3002\u8fd9\u4e2a\u8fc7\u7a0b\u4e2d\uff0c\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u91cf\u662f\u4ece\u4f3d\u9a6c\u5206\u5e03\u4e2d\u6a21\u62df\u51fa\u6765\u7684\uff0c\u7136\u540e\u7528\u751f\u7269\u5b66\u53d8\u5f02\u7cfb\u6570\u6765\u8c03\u6574\uff0c\u4ee5\u7b26\u5408\u5747\u503c-\u65b9\u5dee\u7684\u5173\u7cfb\u3002Splat\u8fd8\u80fd\u6a21\u62df\u90a3\u4e9b\u8868\u8fbe\u91cf\u5f02\u5e38\u7684\u57fa\u56e0\u548c\u968f\u673a\u7684dropout\u73b0\u8c61\uff0c\u6bcf\u4e2a\u7ec6\u80de\u7684\u5e93\u5927\u5c0f\u4e5f\u662f\u6839\u636e\u5bf9\u6570\u6b63\u6001\u5206\u5e03\u6765\u6a21\u62df\u7684\uff0c\u8fd9\u6837\u5c31\u80fd\u66f4\u597d\u5730\u5339\u914d\u771f\u5b9e\u6570\u636e\u96c6\u3002<\/p>\n\n\n\n<p>\u66f4\u9177\u7684\u662f\uff0cSplat\u8fd8\u80fd\u6a21\u62df\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u7684\u8868\u8fbe\u5dee\u5f02\uff0c\u6216\u8005\u7ec6\u80de\u5206\u5316\u8fc7\u7a0b\u4e2d\u8868\u8fbe\u7684\u8fde\u7eed\u53d8\u5316\u3002\u8fd9\u4e9b\u7ec6\u8282\u6211\u4eec\u5728\u540e\u9762\u6a21\u62df\u8ba1\u6570\u7684\u90e8\u5206\u518d\u8be6\u7ec6\u8bf4\u3002\u653e\u5fc3\uff0c\u867d\u7136\u542c\u8d77\u6765\u6709\u70b9\u590d\u6742\uff0c\u4f46\u5b9e\u9645\u64cd\u4f5c\u8d77\u6765\u5c31\u7b80\u5355\u591a\u4e86\u3002\u901a\u8fc7\u6a21\u62df\u6570\u636e\uff0c\u6211\u4eec\u53ef\u4ee5\u5728\u4e0d\u63a5\u89e6\u771f\u5b9e\u6837\u672c\u7684\u60c5\u51b5\u4e0b\uff0c\u6d4b\u8bd5\u6211\u4eec\u7684\u5206\u6790\u65b9\u6cd5\uff0c\u8fd9\u5bf9\u4e8e\u7814\u7a76\u7684\u524d\u671f\u51c6\u5907\u6765\u8bf4\u975e\u5e38\u6709\u5e2e\u52a9\u3002<\/p>\n\n\n\n<p><strong>\u4e09\u3001<\/strong><strong>SplatParams\u5bf9\u8c61\uff1a\u6a21\u62df\u53c2\u6570\u7684\u5b9d\u5e93<\/strong><\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u5c0f\u5e08\u59b9\u8981\u7ed9\u5927\u5bb6\u5c55\u793a\u7684\u662fSplatter\u6a21\u62df\u4e2d\u975e\u5e38\u6838\u5fc3\u7684\u90e8\u5206\u2014\u2014`SplatParams`\u5bf9\u8c61\u3002\u8fd9\u4e2a\u5bf9\u8c61\u5c31\u50cf\u662f\u6211\u4eec\u7684\u6a21\u62df\u53c2\u6570\u7684\u5c0f\u5b9d\u5e93\uff0c\u91cc\u9762\u5b58\u50a8\u4e86\u6240\u6709\u6a21\u62df\u9700\u8981\u7684\u53c2\u6570\u3002\u8ba9\u6211\u4eec\u6765\u521b\u5efa\u4e00\u4e2a\uff0c\u770b\u770b\u5b83\u957f\u4ec0\u4e48\u6837\u5427\u3002<\/p>\n\n\n\n<p>params &lt;- newSplatParams()<\/p>\n\n\n\n<p>params<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"303\" height=\"351\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097063138_77C76A97-DFED-4c47-AE62-0257BB77FDB9.png?resize=303%2C351\" alt=\"\" class=\"wp-image-61256\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097063138_77C76A97-DFED-4c47-AE62-0257BB77FDB9.png?w=303 303w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097063138_77C76A97-DFED-4c47-AE62-0257BB77FDB9.png?resize=259%2C300 259w\" sizes=\"(max-width: 303px) 100vw, 303px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6267\u884c\u4e0a\u9762\u7684\u4ee3\u7801\u540e\uff0c\u6211\u4eec\u4f1a\u5f97\u5230\u4e00\u4e2a`SplatParams`\u7c7b\u7684\u53c2\u6570\u5bf9\u8c61\uff0c\u91cc\u9762\u5305\u542b\u4e86\u57fa\u56e0\u6570\u91cf\u3001\u7ec6\u80de\u6570\u91cf\u3001\u968f\u673a\u79cd\u5b50\u7b49\u5168\u5c40\u53c2\u6570\uff0c\u8fd8\u6709\u6279\u6b21\u6548\u5e94\u3001\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u3001\u5e93\u5927\u5c0f\u3001\u8868\u8fbe\u91cf\u5f02\u5e38\u57fa\u56e0\u3001\u7ec4\u522b\u3001\u5dee\u5f02\u8868\u8fbe\u3001BCV\uff08\u751f\u7269\u5b66\u53d8\u5f02\u7cfb\u6570\uff09\u3001dropout\uff08\u6570\u636e\u4e22\u5931\uff09\u548c\u8def\u5f84\u7b49\u4e00\u5927\u5806\u53c2\u6570\u3002\u8fd9\u4e9b\u53c2\u6570\u4e2d\uff0c\u6709\u4e9b\u662f\u53ef\u4ee5\u4f30\u7b97\u7684\uff0c\u6709\u4e9b\u662f\u56fa\u5b9a\u7684\uff0c\u8fd8\u6709\u4e9b\u662f\u53ef\u4ee5\u8c03\u6574\u7684\u3002<\/p>\n\n\n\n<p><strong>\u83b7\u53d6\u548c\u8bbe\u7f6e\u53c2\u6570\uff1a\u5b9a\u5236\u4f60\u7684\u6a21\u62df<\/strong><\/p>\n\n\n\n<p>\u5982\u679c\u4f60\u60f3\u8981\u67e5\u770b\u6216\u4fee\u6539\u67d0\u4e2a\u7279\u5b9a\u53c2\u6570\uff0c\u6bd4\u5982\u6a21\u62df\u7684\u57fa\u56e0\u6570\u91cf\uff0c\u53ef\u4ee5\u7528`getParam`\u51fd\u6570\u6765\u83b7\u53d6\uff0c\u7528`setParam`\u51fd\u6570\u6765\u8bbe\u7f6e\u65b0\u503c\u3002<\/p>\n\n\n\n<p># \u67e5\u770b\u6a21\u62df\u7684\u57fa\u56e0\u6570\u91cf<\/p>\n\n\n\n<p>getParam(params, &#8220;nGenes&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"216\" height=\"30\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097075700_EE2D95B2-CC0D-498e-909B-D52593EF5FD2.png?resize=216%2C30\" alt=\"\" class=\"wp-image-61257\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p># \u8bbe\u7f6e\u6a21\u62df\u7684\u57fa\u56e0\u6570\u91cf\u4e3a5000<\/p>\n\n\n\n<p>params &lt;- setParam(params, &#8220;nGenes&#8221;, 5000)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"212\" height=\"30\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097086756_B3C68DBE-7C97-40c7-AE9C-25922123FBAE.png?resize=212%2C30\" alt=\"\" class=\"wp-image-61258\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u5982\u679c\u4f60\u60f3\u4e00\u6b21\u8bbe\u7f6e\u591a\u4e2a\u53c2\u6570\uff0c\u53ef\u4ee5\u7528`getParams`\u6216`setParams`\u51fd\u6570\u3002<\/p>\n\n\n\n<p># \u4e00\u6b21\u6027\u8bbe\u7f6e\u591a\u4e2a\u53c2\u6570\uff08\u4f7f\u7528\u5217\u8868\uff09<\/p>\n\n\n\n<p>params &lt;- setParams(params, update = list(nGenes = 8000, mean.rate = 0.5))<\/p>\n\n\n\n<p># \u4f5c\u4e3a\u5217\u8868\u63d0\u53d6\u591a\u4e2a\u53c2\u6570<\/p>\n\n\n\n<p>getParams(params, c(&#8220;nGenes&#8221;, &#8220;mean.rate&#8221;, &#8220;mean.shape&#8221;))<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"432\" height=\"134\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097095478_FBE596BA-F924-4aa2-95E8-6D09A8BF6989.png?resize=432%2C134\" alt=\"\" class=\"wp-image-61259\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097095478_FBE596BA-F924-4aa2-95E8-6D09A8BF6989.png?w=432 432w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097095478_FBE596BA-F924-4aa2-95E8-6D09A8BF6989.png?resize=300%2C93 300w\" sizes=\"(max-width: 432px) 100vw, 432px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p># \u4e00\u6b21\u6027\u8bbe\u7f6e\u591a\u4e2a\u53c2\u6570\uff08\u4f7f\u7528\u989d\u5916\u7684\u53c2\u6570\uff09<\/p>\n\n\n\n<p>params &lt;- setParams(params, mean.shape = 0.5, de.prob = 0.2)<\/p>\n\n\n\n<p>Params<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"293\" height=\"338\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097104433_C88230E2-3FD7-4968-8B54-9FF95854CB56.png?resize=293%2C338\" alt=\"\" class=\"wp-image-61260\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097104433_C88230E2-3FD7-4968-8B54-9FF95854CB56.png?w=293 293w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097104433_C88230E2-3FD7-4968-8B54-9FF95854CB56.png?resize=260%2C300 260w\" sizes=\"(max-width: 293px) 100vw, 293px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6539\u53d8\u4e86\u7684\u53c2\u6570\u4f1a\u4ee5\u5927\u5199\u5b57\u6bcd\u663e\u793a\uff0c\u8fd9\u6837\u6211\u4eec\u5c31\u77e5\u9053\u5b83\u4eec\u5df2\u7ecf\u88ab\u5b9a\u5236\u8fc7\u4e86\uff0c\u4e0d\u518d\u662f\u9ed8\u8ba4\u503c\u3002<\/p>\n\n\n\n<p># \u76f4\u63a5\u5728\u521b\u5efa\u65f6\u8bbe\u7f6e\u53c2\u6570<\/p>\n\n\n\n<p>params &lt;- newSplatParams(lib.loc = 12, lib.scale = 0.6)<\/p>\n\n\n\n<p>getParams(params, c(&#8220;lib.loc&#8221;, &#8220;lib.scale&#8221;))<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"338\" height=\"88\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097114333_2CB590B6-4FBF-49f4-8337-9E5C77F585D3.png?resize=338%2C88\" alt=\"\" class=\"wp-image-61261\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097114333_2CB590B6-4FBF-49f4-8337-9E5C77F585D3.png?w=338 338w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097114333_2CB590B6-4FBF-49f4-8337-9E5C77F585D3.png?resize=300%2C78 300w\" sizes=\"(max-width: 338px) 100vw, 338px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u901a\u8fc7\u8fd9\u79cd\u65b9\u5f0f\uff0c\u6211\u4eec\u53ef\u4ee5\u8f7b\u677e\u5730\u5b9a\u5236\u6211\u4eec\u7684\u6a21\u62df\u53c2\u6570\uff0c\u8ba9\u6a21\u62df\u6570\u636e\u66f4\u8d34\u8fd1\u6211\u4eec\u7814\u7a76\u7684\u9700\u6c42\u3002\u662f\u4e0d\u662f\u5f88\u65b9\u4fbf\u5462\uff1f<\/p>\n\n\n\n<p><strong>\u56db\u3001<\/strong><strong>\u53c2\u6570\u4f30\u7b97\uff1a\u8ba9\u6a21\u62df\u66f4\u7cbe\u51c6<\/strong><\/p>\n\n\n\n<p>\u4f60\u77e5\u9053\u4e48\uff0cSplatter\u5305\u7684`splatEstimate`\u51fd\u6570\u80fd\u5e2e\u6211\u4eec\u4ece\u542b\u6709\u8ba1\u6570\u6570\u636e\u7684\u96c6\u5408\u4e2d\u4f30\u7b97\u51fa\u8bb8\u591a\u53c2\u6570\u3002\u8fd9\u5c31\u50cf\u662f\u7ed9\u6a21\u62df\u6570\u636e\u88c5\u4e0a\u4e86\u4e00\u4e2a\u7cbe\u51c6\u7684\u6307\u5357\u9488\uff0c\u8ba9\u5b83\u66f4\u8d34\u8fd1\u771f\u5b9e\u4e16\u754c\u7684\u6570\u636e\u3002\u4e0b\u9762\uff0c\u5c31\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770b\u8fd9\u795e\u5947\u7684\u6b65\u9aa4\u5427\uff01<\/p>\n\n\n\n<p>\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u83b7\u53d6\u4e00\u4e2a\u6a21\u62df\u7684\u8ba1\u6570\u77e9\u9635\u3002\u8fd9\u91cc\u6211\u4eec\u7528`scater`\u5305\u7684`mockSCE`\u51fd\u6570\u6765\u751f\u6210\u4e00\u4e2a\u6a21\u62df\u7684\u5355\u7ec6\u80de\u6570\u636e\u5bf9\u8c61`sce`\uff0c\u7136\u540e\u4ece\u4e2d\u63d0\u53d6\u8ba1\u6570\u77e9\u9635\u3002<\/p>\n\n\n\n<p># \u83b7\u53d6\u6a21\u62df\u7684\u8ba1\u6570\u77e9\u9635<\/p>\n\n\n\n<p>counts &lt;- counts(sce)<\/p>\n\n\n\n<p># \u68c0\u67e5counts\u662f\u5426\u4e3a\u6574\u6570\u77e9\u9635<\/p>\n\n\n\n<p>class(counts)<\/p>\n\n\n\n<p>typeof(counts)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"176\" height=\"59\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097125855_C4E50797-01D7-4353-9168-2BDDE8B45B1C.png?resize=176%2C59\" alt=\"\" class=\"wp-image-61262\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p># \u67e5\u770b\u7ef4\u5ea6\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u57fa\u56e0\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u7ec6\u80de<\/p>\n\n\n\n<p>dim(counts)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"104\" height=\"30\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097136180_38F79B22-16ED-4a4d-BF56-A7907E3D42E7.png?resize=104%2C30\" alt=\"\" class=\"wp-image-61263\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097136180_38F79B22-16ED-4a4d-BF56-A7907E3D42E7.png?w=104 104w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097136180_38F79B22-16ED-4a4d-BF56-A7907E3D42E7.png?resize=100%2C30 100w\" sizes=\"(max-width: 104px) 100vw, 104px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7\u67e5\u770b\u77e9\u9635\u7684\u524d\u51e0\u884c\u6765\u4e86\u89e3\u6570\u636e\u7684\u6982\u8c8c\u3002\u8fd9\u4e2a\u8ba1\u6570\u77e9\u9635\u662f\u4e00\u4e2a\u6574\u6570\u77e9\u9635\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u57fa\u56e0\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u7ec6\u80de\u3002<\/p>\n\n\n\n<p># \u663e\u793a\u524d\u51e0\u9879\u6570\u636e<\/p>\n\n\n\n<p>counts[1:5, 1:5]<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"420\" height=\"100\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097144845_666EA08B-CC7A-4b16-98F6-33E69FBDA995.png?resize=420%2C100\" alt=\"\" class=\"wp-image-61264\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097144845_666EA08B-CC7A-4b16-98F6-33E69FBDA995.png?w=420 420w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097144845_666EA08B-CC7A-4b16-98F6-33E69FBDA995.png?resize=300%2C71 300w\" sizes=\"(max-width: 420px) 100vw, 420px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u5c31\u662f\u91cd\u5934\u620f\u2014\u2014\u53c2\u6570\u4f30\u7b97\u4e86\u3002\u6211\u4eec\u4f1a\u7528`splatEstimate`\u51fd\u6570\u6765\u5b8c\u6210\u8fd9\u4e2a\u4efb\u52a1\u3002<\/p>\n\n\n\n<p># \u53c2\u6570\u4f30\u7b97<\/p>\n\n\n\n<p>params &lt;- splatEstimate(counts)<\/p>\n\n\n\n<p>\u8fd9\u4e2a\u8fc7\u7a0b\u5305\u62ec\u51e0\u4e2a\u6b65\u9aa4\uff1a<\/p>\n\n\n\n<p>1. \u5e73\u5747\u53c2\u6570\uff1a\u901a\u8fc7\u62df\u5408\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u7684\u4f3d\u9a6c\u5206\u5e03\u6765\u4f30\u7b97\u3002<\/p>\n\n\n\n<p>2. \u5e93\u5927\u5c0f\u53c2\u6570\uff1a\u901a\u8fc7\u62df\u5408\u5e93\u5927\u5c0f\u7684\u5bf9\u6570\u6b63\u6001\u5206\u5e03\u6765\u4f30\u7b97\u3002<\/p>\n\n\n\n<p>3. \u8868\u8fbe\u91cf\u5f02\u5e38\u53c2\u6570\uff1a\u901a\u8fc7\u786e\u5b9a\u5f02\u5e38\u503c\u7684\u6570\u91cf\uff0c\u5e76\u62df\u5408\u8fd9\u4e9b\u5f02\u5e38\u503c\u4e0e\u4e2d\u4f4d\u6570\u5dee\u5f02\u7684\u5bf9\u6570\u6b63\u6001\u5206\u5e03\u6765\u4f30\u7b97\u3002<\/p>\n\n\n\n<p>4. BCV\u53c2\u6570\uff1a\u4f7f\u7528`edgeR`\u5305\u4e2d\u7684`estimateDisp`\u51fd\u6570\u6765\u4f30\u7b97\u3002<\/p>\n\n\n\n<p>5. Dropout\u53c2\u6570\uff1a\u901a\u8fc7\u68c0\u67e5dropout\u73b0\u8c61\u662f\u5426\u5b58\u5728\uff0c\u5e76\u62df\u5408\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u4e0e\u96f6\u503c\u6bd4\u4f8b\u4e4b\u95f4\u7684\u5173\u7cfb\u7684\u903b\u8f91\u51fd\u6570\u6765\u4f30\u7b97\u3002<\/p>\n\n\n\n<p>\u901a\u8fc7\u8fd9\u4e9b\u6b65\u9aa4\uff0c\u6211\u4eec\u5c31\u80fd\u83b7\u5f97\u4e00\u7ec4\u8d34\u8fd1\u771f\u5b9e\u6570\u636e\u7684\u53c2\u6570\uff0c\u7528\u5b83\u4eec\u6765\u6a21\u62df\u65b0\u7684\u6570\u636e\u96c6\uff0c\u662f\u4e0d\u662f\u5f88\u68d2\u5462\uff1f\u8fd9\u6837\u4e00\u6765\uff0c\u6211\u4eec\u5c31\u80fd\u5728\u4e0d\u63a5\u89e6\u771f\u5b9e\u6837\u672c\u7684\u60c5\u51b5\u4e0b\uff0c\u6d4b\u8bd5\u548c\u9a8c\u8bc1\u6211\u4eec\u7684\u5206\u6790\u65b9\u6cd5\u4e86\u3002<\/p>\n\n\n\n<p><strong>\u4e94\u3001<\/strong><strong>\u6a21\u62df\u8ba1\u6570\uff1a\u7528`splatSimulate`\u751f\u6210\u6570\u636e<\/strong><\/p>\n\n\n\n<p>\u5f53\u6211\u4eec\u5bf9\u4e00\u7ec4\u53c2\u6570\u611f\u5230\u6ee1\u610f\u540e\uff0c\u5c31\u53ef\u4ee5\u7528\u8fd9\u4e9b\u53c2\u6570\u6765\u751f\u6210\u65b0\u7684\u6570\u636e\u96c6\u4e86\u3002\u5982\u679c\u6211\u4eec\u60f3\u8981\u5fae\u8c03\u8fd9\u4e9b\u53c2\u6570\uff0c\u53ef\u4ee5\u76f4\u63a5\u5728\u51fd\u6570\u4e2d\u63d0\u4f9b\u5b83\u4eec\uff1b\u5982\u679c\u6211\u4eec\u4e0d\u63d0\u4f9b\u4efb\u4f55\u53c2\u6570\uff0c\u5c31\u4f1a\u4f7f\u7528\u9ed8\u8ba4\u503c\u3002<\/p>\n\n\n\n<p>sim &lt;- splatSimulate(params, nGenes = 1000)<\/p>\n\n\n\n<p>sim<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"318\" height=\"123\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097154765_49A1E7B9-2D6E-476f-9E83-C0D2D7A69123.png?resize=318%2C123\" alt=\"\" class=\"wp-image-61265\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097154765_49A1E7B9-2D6E-476f-9E83-C0D2D7A69123.png?w=318 318w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097154765_49A1E7B9-2D6E-476f-9E83-C0D2D7A69123.png?resize=300%2C116 300w\" sizes=\"(max-width: 318px) 100vw, 318px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6267\u884c\u4e0a\u9762\u7684\u4ee3\u7801\u540e\uff0c\u6211\u4eec\u4f1a\u5f97\u5230\u4e00\u4e2a`SingleCellExperiment`\u5bf9\u8c61\uff0c\u91cc\u9762\u5305\u542b\u4e861000\u4e2a\u7279\u5f81\uff08\u57fa\u56e0\uff09\u548c200\u4e2a\u6837\u672c\uff08\u7ec6\u80de\uff09\u3002\u8fd9\u4e2a\u5bf9\u8c61\u7684\u4e3b\u8981\u90e8\u5206\u662f\u4e00\u4e2a\u7279\u5f81\u4e58\u4ee5\u6837\u672c\u7684\u77e9\u9635\uff0c\u5305\u542b\u4e86\u6a21\u62df\u7684\u8ba1\u6570\u6570\u636e\uff0c\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7`counts`\u6765\u8bbf\u95ee\u8fd9\u4e9b\u6570\u636e\u3002\u6b64\u5916\uff0c\u8fd9\u4e2a\u5bf9\u8c61\u8fd8\u53ef\u4ee5\u5305\u542b\u5176\u4ed6\u8868\u8fbe\u91cf\u5ea6\u91cf\uff0c\u6bd4\u5982FPKM\u6216TPM\u3002\u6b64\u5916\uff0c`SingleCellExperiment`\u5bf9\u8c61\u8fd8\u5305\u542b\u4e86\u6bcf\u4e2a\u7ec6\u80de\u7684\u8868\u578b\u4fe1\u606f\uff08\u901a\u8fc7`colData`\u8bbf\u95ee\uff09\u548c\u6bcf\u4e2a\u57fa\u56e0\u7684\u7279\u5f81\u4fe1\u606f\uff08\u901a\u8fc7`rowData`\u8bbf\u95ee\uff09\u3002Splatter\u5229\u7528\u8fd9\u4e9b\u63d2\u69fd\u4ee5\u53ca`assays`\u6765\u5b58\u50a8\u6a21\u62df\u8fc7\u7a0b\u4e2d\u7684\u4e2d\u95f4\u503c\u3002<\/p>\n\n\n\n<p># \u8bbf\u95ee\u8ba1\u6570\u6570\u636e<\/p>\n\n\n\n<p>counts(sim)[1:5, 1:5]<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"208\" height=\"74\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097164941_A5424AE9-314E-4c79-AB8B-C4CD5A270278.png?resize=208%2C74\" alt=\"\" class=\"wp-image-61266\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u6211\u4eec\u53ef\u4ee5\u8bbf\u95ee\u5173\u4e8e\u57fa\u56e0\u7684\u4fe1\u606f\uff0c\u6bd4\u5982\u57fa\u7840\u57fa\u56e0\u5747\u503c\u3001\u5f02\u5e38\u56e0\u5b50\u548c\u57fa\u56e0\u5747\u503c\u7b49\u3002<\/p>\n\n\n\n<p># \u57fa\u56e0\u4fe1\u606f<\/p>\n\n\n\n<p>head(rowData(sim))<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"286\" height=\"99\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097175260_531DE385-B6AB-45cf-8A9A-3B573BB4D3C9.png?resize=286%2C99\" alt=\"\" class=\"wp-image-61267\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u540c\u6837\uff0c\u6211\u4eec\u4e5f\u53ef\u4ee5\u83b7\u53d6\u5173\u4e8e\u7ec6\u80de\u7684\u4fe1\u606f\uff0c\u6bd4\u5982\u6bcf\u4e2a\u7ec6\u80de\u6240\u5c5e\u7684\u7ec4\u6216\u8def\u5f84\u3001\u9884\u671f\u7684\u5e93\u5927\u5c0f\u7b49\u3002<\/p>\n\n\n\n<p># \u7ec6\u80de\u4fe1\u606f<\/p>\n\n\n\n<p>head(colData(sim))<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"249\" height=\"118\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097186238_98E50012-5377-4fe0-BD27-7B727665FA26.png?resize=249%2C118\" alt=\"\" class=\"wp-image-61268\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u6b64\u5916\uff0c\u6211\u4eec\u8fd8\u53ef\u4ee5\u67e5\u770b\u57fa\u56e0\u4e0e\u7ec6\u80de\u4e4b\u95f4\u7684\u77e9\u9635\u4fe1\u606f\uff0c\u6bd4\u5982\u6bcf\u4e2a\u57fa\u56e0\u5728\u6bcf\u4e2a\u7ec6\u80de\u4e2d\u7684\u8868\u8fbe\u5747\u503c\u3001\u751f\u7269\u5b66\u53d8\u5f02\u7cfb\u6570\uff08BCV\uff09\u3001\u7ec6\u80de\u5747\u503c\u3001\u771f\u5b9e\u8ba1\u6570\u548cdropout\u4fe1\u606f\u7b49\u3002<\/p>\n\n\n\n<p># \u57fa\u56e0\u4e0e\u7ec6\u80de\u77e9\u9635\u4fe1\u606f<\/p>\n\n\n\n<p>names(assays(sim))<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"25\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097196739_765B5871-577D-483e-8F27-6187827A4F80.png?resize=554%2C25\" alt=\"\" class=\"wp-image-61269\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097196739_765B5871-577D-483e-8F27-6187827A4F80.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097196739_765B5871-577D-483e-8F27-6187827A4F80.png?resize=300%2C14 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6211\u4eec\u8fd8\u53ef\u4ee5\u5f97\u5230\u7ec6\u80de\u5747\u503c\u77e9\u9635\uff0c\u5e76\u67e5\u770b\u524d\u51e0\u884c\u548c\u524d\u51e0\u5217\u7684\u6570\u636e\uff1a<\/p>\n\n\n\n<p>assays(sim)$CellMeans[1:5, 1:5]<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"342\" height=\"80\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097208060_1BD0681F-2F43-4eb4-AA48-A3806AC6BBDC.png?resize=342%2C80\" alt=\"\" class=\"wp-image-61270\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097208060_1BD0681F-2F43-4eb4-AA48-A3806AC6BBDC.png?w=342 342w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097208060_1BD0681F-2F43-4eb4-AA48-A3806AC6BBDC.png?resize=300%2C70 300w\" sizes=\"(max-width: 342px) 100vw, 342px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6267\u884c\u8fd9\u4e2a\u547d\u4ee4\u540e\uff0c\u6211\u4eec\u4f1a\u5f97\u5230\u4e00\u4e2a\u77e9\u9635\uff0c\u91cc\u9762\u5305\u542b\u4e86\u4e94\u4e2a\u57fa\u56e0\uff08Gene1\u5230Gene5\uff09\u5728\u4e94\u4e2a\u7ec6\u80de\uff08Cell1\u5230Cell5\uff09\u4e2d\u7684\u8868\u8fbe\u5747\u503c\u3002\u8fd9\u4e9b\u6570\u503c\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u7406\u89e3\u57fa\u56e0\u5728\u4e0d\u540c\u7ec6\u80de\u4e2d\u7684\u8868\u8fbe\u6a21\u5f0f\u3002<\/p>\n\n\n\n<p>\u4f7f\u7528`SingleCellExperiment`\u5bf9\u8c61\u7684\u53e6\u4e00\u4e2a\u5927\u597d\u5904\u662f\uff0c\u6211\u4eec\u53ef\u4ee5\u7acb\u5373\u4f7f\u7528\u5176\u4ed6\u5206\u6790\u5305\uff0c\u6bd4\u5982`scater`\u5305\u4e2d\u7684\u7ed8\u56fe\u51fd\u6570\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u5236\u4f5c<a>PCA\u56fe<\/a>\u6765\u53ef\u89c6\u5316\u6570\u636e\u3002<\/p>\n\n\n\n<p># \u4f7f\u7528scater\u8ba1\u7b97logcounts\u5e76\u7ed8\u5236PCA\u56fe<\/p>\n\n\n\n<p>sim &lt;- logNormCounts(sim)<\/p>\n\n\n\n<p>sim &lt;- runPCA(sim)<\/p>\n\n\n\n<p>plotPCA(sim)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"298\" height=\"216\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097218029_B347502A-31D2-4390-A8D5-15E659769AB3.png?resize=298%2C216\" alt=\"\" class=\"wp-image-61271\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u6ce8\u610f\uff1a\u7531\u4e8e\u6a21\u62df\u662f\u968f\u673a\u7684\uff0c\u6bcf\u6b21\u8fd0\u884c\u7684\u7ed3\u679c\u53ef\u80fd\u4f1a\u6709\u6240\u4e0d\u540c\u3002<\/p>\n\n\n\n<p>\u901a\u8fc7\u8fd9\u4e9b\u6b65\u9aa4\uff0c\u6211\u4eec\u5c31\u80fd\u751f\u6210\u4e00\u4e2a\u5305\u542b\u4e30\u5bcc\u4fe1\u606f\u7684\u6a21\u62df\u6570\u636e\u96c6\uff0c\u5e76\u4e14\u53ef\u4ee5\u5229\u7528\u73b0\u6709\u7684\u5206\u6790\u5de5\u5177\u8fdb\u884c\u8fdb\u4e00\u6b65\u7684\u5206\u6790\u3002\u662f\u4e0d\u662f\u611f\u89c9Splatter\u5305\u8d85\u7ea7\u5f3a\u5927\u5462\uff1f\u5982\u679c\u4f60\u5728\u6a21\u62df\u6570\u636e\u7684\u8fc7\u7a0b\u4e2d\u6709\u4efb\u4f55\u7591\u95ee\uff0c\u8bb0\u5f97\u627e\u5c0f\u5e08\u59b9\u5e2e\u5fd9\u54e6\uff01<\/p>\n\n\n\n<p><strong>\u6a21\u62df\u7ec6\u80de\u7fa4\u7ec4<\/strong><\/p>\n\n\n\n<p>\u60f3\u8c61\u4e00\u4e0b\uff0c\u6211\u4eec\u4e0d\u4ec5\u60f3\u7814\u7a76\u5355\u4e00\u7c7b\u578b\u7684\u7ec6\u80de\uff0c\u8fd8\u60f3\u770b\u770b\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u6df7\u5408\u5728\u4e00\u8d77\u65f6\u4f1a\u53d1\u751f\u4ec0\u4e48\u3002Splatter\u5305\u53ef\u4ee5\u901a\u8fc7\u6539\u53d8`method`\u53c2\u6570\u6765\u6a21\u62df\u8fd9\u79cd\u60c5\u51b5\u3002\u6bd4\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u8bbe\u7f6e`group.prob`\u53c2\u6570\uff0c\u5e76\u628a`method`\u53c2\u6570\u8bbe\u4e3a&#8221;groups&#8221;\u6765\u6a21\u62df\u4e24\u7ec4\u7ec6\u80de\u3002<\/p>\n\n\n\n<p>sim.groups &lt;- splatSimulate(<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;group.prob = c(0.5, 0.5),<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;method = &#8220;groups&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;verbose = FALSE)<\/p>\n\n\n\n<p>sim.groups &lt;- logNormCounts(sim.groups)<\/p>\n\n\n\n<p>sim.groups &lt;- runPCA(sim.groups)<\/p>\n\n\n\n<p>plotPCA(sim.groups, colour_by = &#8220;Group&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"306\" height=\"222\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097230893_60EB399C-C287-4cd3-8C70-E7DE16413C3E.png?resize=306%2C222\" alt=\"\" class=\"wp-image-61272\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097230893_60EB399C-C287-4cd3-8C70-E7DE16413C3E.png?w=306 306w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097230893_60EB399C-C287-4cd3-8C70-E7DE16413C3E.png?resize=300%2C218 300w\" sizes=\"(max-width: 306px) 100vw, 306px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5982\u679c\u6211\u4eec\u628a\u4e24\u7ec4\u7ec6\u80de\u7684\u6982\u7387\u90fd\u8bbe\u4e3a0.5\uff0c\u90a3\u4e48\u6211\u4eec\u5e94\u8be5\u80fd\u5f97\u5230\u5927\u7ea6\u76f8\u7b49\u6570\u91cf\u7684\u7ec6\u80de\uff08\u5728\u8fd9\u4e2a\u4f8b\u5b50\u4e2d\u5927\u7ea6\u662f50\u4e2a\uff09\u3002\u5982\u679c\u6211\u4eec\u60f3\u8981\u4e0d\u7b49\u6570\u91cf\u7684\u7ec6\u80de\u7fa4\uff0c\u6211\u4eec\u53ef\u4ee5\u628a`group.prob`\u8bbe\u4e3a\u4efb\u4f55\u52a0\u8d77\u6765\u7b49\u4e8e1\u7684\u6982\u7387\u96c6\u5408\u3002<\/p>\n\n\n\n<p><strong>\u6a21\u62df\u5206\u5316\u8def\u5f84<\/strong><\/p>\n\n\n\n<p>\u53e6\u4e00\u4e2a\u6211\u4eec\u7ecf\u5e38\u611f\u5174\u8da3\u7684\u60c5\u51b5\u662f\u7ec6\u80de\u5206\u5316\u8fc7\u7a0b\uff0c\u5176\u4e2d\u4e00\u4e2a\u7ec6\u80de\u7c7b\u578b\u9010\u6e10\u8f6c\u53d8\u4e3a\u53e6\u4e00\u79cd\u7c7b\u578b\u3002Splatter\u901a\u8fc7\u6a21\u62df\u4e24\u7ec4\u4e4b\u95f4\u7684\u4e00\u7cfb\u5217\u6b65\u9aa4\uff0c\u5e76\u968f\u673a\u5c06\u6bcf\u4e2a\u7ec6\u80de\u5206\u914d\u7ed9\u4e00\u4e2a\u6b65\u9aa4\u6765\u8fd1\u4f3c\u8fd9\u4e2a\u8fc7\u7a0b\u3002\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528&#8221;paths&#8221;\u65b9\u6cd5\u6765\u521b\u5efa\u8fd9\u79cd\u6a21\u62df\u3002<\/p>\n\n\n\n<p>sim.paths &lt;- splatSimulate(<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;de.prob = 0.2,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;nGenes = 1000,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;method = &#8220;paths&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;verbose = FALSE)<\/p>\n\n\n\n<p>sim.paths &lt;- logNormCounts(sim.paths)<\/p>\n\n\n\n<p>sim.paths &lt;- runPCA(sim.paths)<\/p>\n\n\n\n<p>plotPCA(sim.paths, colour_by = &#8220;Step&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"283\" height=\"206\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097263613_39625272-BFC5-437a-9ABF-8B5C33A6C44C.png?resize=283%2C206\" alt=\"\" class=\"wp-image-61273\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u5728\u8fd9\u91cc\uff0c\u989c\u8272\u4ee3\u8868\u4e86\u6bcf\u4e2a\u7ec6\u80de\u5728\u5206\u5316\u8def\u5f84\u4e0a\u7684\u201c\u6b65\u9aa4\u201d\u3002\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u989c\u8272\u8f83\u6df1\u7684\u7ec6\u80de\u66f4\u63a5\u8fd1\u539f\u59cb\u7ec6\u80de\u7c7b\u578b\uff0c\u800c\u989c\u8272\u8f83\u6d45\u7684\u7ec6\u80de\u66f4\u63a5\u8fd1\u6700\u7ec8\u5206\u5316\u7684\u7ec6\u80de\u7c7b\u578b\u3002\u901a\u8fc7\u8bbe\u7f6e\u989d\u5916\u7684\u53c2\u6570\uff0c\u6211\u4eec\u53ef\u4ee5\u6a21\u62df\u66f4\u590d\u6742\u7684\u8fc7\u7a0b\uff08\u4f8b\u5982\uff0c\u4ece\u5355\u4e00\u7956\u7ec6\u80de\u5206\u5316\u51fa\u591a\u79cd\u6210\u719f\u7ec6\u80de\u7c7b\u578b\uff09\u3002<\/p>\n\n\n\n<p><strong>\u6279\u6b21\u6548\u5e94<\/strong><\/p>\n\n\n\n<p>\u5728\u4efb\u4f55\u6d4b\u5e8f\u5b9e\u9a8c\u7684\u5206\u6790\u4e2d\uff0c\u6279\u6b21\u6548\u5e94\u90fd\u662f\u4e00\u4e2a\u91cd\u8981\u56e0\u7d20\uff0c\u8fd9\u662f\u540c\u4e00\u65f6\u95f4\u5904\u7406\u7684\u4e00\u7ec4\u6837\u672c\u4e2d\u5e38\u89c1\u7684\u6280\u672f\u53d8\u5f02\u3002\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7\u544a\u8bc9Splatter\u6bcf\u4e2a\u6279\u6b21\u4e2d\u6709\u591a\u5c11\u4e2a\u7ec6\u80de\u6765\u5e94\u7528\u6279\u6b21\u6548\u5e94\u3002<\/p>\n\n\n\n<p>sim.batches &lt;- splatSimulate(batchCells = c(50, 50), verbose = FALSE)<\/p>\n\n\n\n<p>sim.batches &lt;- logNormCounts(sim.batches)<\/p>\n\n\n\n<p>sim.batches &lt;- runPCA(sim.batches)<\/p>\n\n\n\n<p>plotPCA(sim.batches, colour_by = &#8220;Batch&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"305\" height=\"222\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097275309_E8D14045-8BC3-4669-8E83-DE46999FA553.png?resize=305%2C222\" alt=\"\" class=\"wp-image-61274\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097275309_E8D14045-8BC3-4669-8E83-DE46999FA553.png?w=305 305w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097275309_E8D14045-8BC3-4669-8E83-DE46999FA553.png?resize=300%2C218 300w\" sizes=\"(max-width: 305px) 100vw, 305px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u8fd9\u770b\u8d77\u6765\u548c\u6211\u4eec\u6a21\u62df\u7fa4\u7ec4\u65f6\u5f88\u50cf\uff0c\u56e0\u4e3a\u8fc7\u7a0b\u975e\u5e38\u76f8\u4f3c\u3002\u4e0d\u540c\u7684\u662f\uff0c\u6279\u6b21\u6548\u5e94\u9002\u7528\u4e8e\u6240\u6709\u57fa\u56e0\uff0c\u4e0d\u4ec5\u4ec5\u662f\u90a3\u4e9b\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\uff0c\u800c\u4e14\u6548\u5e94\u901a\u5e38\u8f83\u5c0f\u3002\u901a\u8fc7\u7ed3\u5408\u7fa4\u7ec4\u548c\u6279\u6b21\uff0c\u6211\u4eec\u53ef\u4ee5\u6a21\u62df\u6211\u4eec\u4e0d\u611f\u5174\u8da3\u7684\u53d8\u5f02\uff08\u6279\u6b21\uff09\u548c\u6211\u4eec\u611f\u5174\u8da3\u7684\u53d8\u5f02\uff08\u7fa4\u7ec4\uff09\u3002<\/p>\n\n\n\n<p><strong>\u6a21\u62df\u4e0d\u540c\u7684\u8868\u8fbe\u503c<\/strong><strong><\/strong><\/p>\n\n\n\n<p>Splatter\u9ed8\u8ba4\u662f\u8bbe\u8ba1\u6765\u6a21\u62df\u8ba1\u6570\u6570\u636e\u7684\uff0c\u4f46\u6709\u4e9b\u5206\u6790\u65b9\u6cd5\u53ef\u80fd\u9700\u8981\u5176\u4ed6\u7c7b\u578b\u7684\u8868\u8fbe\u503c\uff0c\u5c24\u5176\u662f\u957f\u5ea6\u6807\u51c6\u5316\u7684\u503c\uff0c\u6bd4\u5982TPM\u6216FPKM\u3002scater\u5305\u6709\u51fd\u6570\u53ef\u4ee5\u5c06\u8fd9\u4e9b\u503c\u6dfb\u52a0\u5230SingleCellExperiment\u5bf9\u8c61\u4e2d\uff0c\u4f46\u5b83\u4eec\u9700\u8981\u6bcf\u4e2a\u57fa\u56e0\u7684\u957f\u5ea6\u3002\u8fd9\u65f6\uff0c\u6211\u4eec\u53ef\u4ee5\u7528addGeneLengths\u51fd\u6570\u6765\u6a21\u62df\u8fd9\u4e9b\u957f\u5ea6\u3002<\/p>\n\n\n\n<p>sim &lt;- simpleSimulate(verbose = FALSE)<\/p>\n\n\n\n<p>sim &lt;- addGeneLengths(sim)<\/p>\n\n\n\n<p>head(rowData(sim))<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"298\" height=\"144\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097287764_BB6EE779-D9C7-4299-A667-8D7FAB7AC34A.png?resize=298%2C144\" alt=\"\" class=\"wp-image-61275\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u7136\u540e\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u7528scater\u6765\u8ba1\u7b97TPM\u4e86\u3002<\/p>\n\n\n\n<p>tpm(sim) &lt;- calculateTPM(sim, rowData(sim)$Length)<\/p>\n\n\n\n<p>tpm(sim)[1:5, 1:5]<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"400\" height=\"116\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097295940_13FB72F3-5927-48c5-95F8-AB42EE405047.png?resize=400%2C116\" alt=\"\" class=\"wp-image-61276\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097295940_13FB72F3-5927-48c5-95F8-AB42EE405047.png?w=400 400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097295940_13FB72F3-5927-48c5-95F8-AB42EE405047.png?resize=300%2C87 300w\" sizes=\"(max-width: 400px) 100vw, 400px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0caddGeneLengths\u4f7f\u7528\u5bf9\u6570\u6b63\u6001\u5206\u5e03\u751f\u6210\u503c\uff0c\u7136\u540e\u56db\u820d\u4e94\u5165\u5f97\u5230\u6574\u6570\u957f\u5ea6\u3002\u8fd9\u4e2a\u5206\u5e03\u7684\u53c2\u6570\u662f\u57fa\u4e8e\u4eba\u7c7b\u86cb\u767d\u8d28\u7f16\u7801\u57fa\u56e0\u7684\uff0c\u4f46\u5982\u679c\u9700\u8981\uff0c\u4e5f\u53ef\u4ee5\u8c03\u6574\uff08\u6bd4\u5982\u9488\u5bf9\u5176\u4ed6\u7269\u79cd\uff09\u3002\u6216\u8005\uff0c\u4e5f\u53ef\u4ee5\u4ece\u4e00\u4e2a\u63d0\u4f9b\u7684\u5411\u91cf\u4e2d\u62bd\u6837\u957f\u5ea6\u3002<\/p>\n\n\n\n<p><strong>\u7f29\u51cf\u6a21\u62df\u5927\u5c0f<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u5728\u4f7f\u7528Splatter\u5305\u6a21\u62df\u6570\u636e\u65f6\uff0c\u6211\u4eec\u4f1a\u5f97\u5230\u5f88\u591a\u4e2d\u95f4\u503c\uff0c\u8fd9\u4e9b\u503c\u867d\u7136\u6709\u52a9\u4e8e\u8bc4\u4f30\uff0c\u4f46\u4e5f\u4f1a\u5927\u5927\u589e\u52a0\u6570\u636e\u7684\u5927\u5c0f\u3002\u5982\u679c\u4f60\u4e0d\u9700\u8981\u8fd9\u4e9b\u4e2d\u95f4\u503c\uff0c\u6211\u4eec\u53ef\u4ee5\u7528`minimiseSCE()`\u51fd\u6570\u6765\u7f29\u51cf\u6a21\u62df\u6570\u636e\u7684\u5927\u5c0f\uff0c\u975e\u5e38\u5b9e\u7528\u54e6\uff01<\/p>\n\n\n\n<p>\u9996\u5148\uff0c\u6211\u4eec\u8fd0\u884c`splatSimulate()`\u51fd\u6570\u6765\u751f\u6210\u6a21\u62df\u6570\u636e\uff1a<\/p>\n\n\n\n<p>sim &lt;- splatSimulate()<\/p>\n\n\n\n<p>\u7136\u540e\uff0c\u6211\u4eec\u4f7f\u7528`minimiseSCE()`\u51fd\u6570\u6765\u7f29\u51cf\u6570\u636e\u5927\u5c0f\uff1a<\/p>\n\n\n\n<p>minimiseSCE(sim)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"333\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097309117_86E7238A-65BE-401d-A8F8-B58850D57DE0.png?resize=554%2C333\" alt=\"\" class=\"wp-image-61277\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097309117_86E7238A-65BE-401d-A8F8-B58850D57DE0.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097309117_86E7238A-65BE-401d-A8F8-B58850D57DE0.png?resize=300%2C180 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u8fd9\u4e2a\u51fd\u6570\u9ed8\u8ba4\u4f1a\u79fb\u9664`rowData(sce)`\u3001`colData(sce)`\u548c`metadata(sce)`\u4e2d\u7684\u6240\u6709\u5185\u5bb9\uff0c\u53ea\u4fdd\u7559`counts`\u3002\u5982\u679c\u4f60\u6709\u5176\u4ed6\u60f3\u8981\u4fdd\u7559\u7684\u5185\u5bb9\uff0c\u53ef\u4ee5\u5728\u51fd\u6570\u4e2d\u6307\u5b9a\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u4fdd\u7559`Gene`\u3001`Cell`\u548c`Batch`\u5217\uff1a<\/p>\n\n\n\n<p>minimiseSCE(sim,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;rowData.keep = &#8220;Gene&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;colData.keep = c(&#8220;Cell&#8221;, &#8220;Batch&#8221;),<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;metadata.keep = TRUE)<\/p>\n\n\n\n<p>\u8fd9\u6837\uff0c\u6211\u4eec\u5c31\u80fd\u5f97\u5230\u4e00\u4e2a\u66f4\u5c0f\u7684`SingleCellExperiment`\u5bf9\u8c61\uff0c\u540c\u65f6\u4fdd\u7559\u4e86\u6211\u4eec\u5173\u5fc3\u7684\u4fe1\u606f\u3002\u662f\u4e0d\u662f\u5f88\u65b9\u4fbf\u5462\uff1f<\/p>\n\n\n\n<p><strong>\u516d\u3001<\/strong><strong>\u6bd4\u8f83\u6a21\u62df\u6570\u636e\u4e0e\u771f\u5b9e\u6570\u636e<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u5728\u6a21\u62df\u6570\u636e\u751f\u6210\u4e4b\u540e\uff0c\u4f60\u53ef\u80fd\u60f3\u8981\u5c06\u5176\u4e0e\u771f\u5b9e\u6570\u636e\u96c6\u8fdb\u884c\u6bd4\u8f83\uff0c\u6216\u8005\u6bd4\u8f83\u4e0d\u540c\u53c2\u6570\u6216\u6a21\u578b\u4e0b\u7684\u6a21\u62df\u7ed3\u679c\u3002`splat`\u5305\u63d0\u4f9b\u4e86\u4e00\u4e2a\u540d\u4e3a`compareSCEs`\u7684\u51fd\u6570\uff0c\u65e8\u5728\u7b80\u5316\u8fd9\u4e9b\u6bd4\u8f83\u5de5\u4f5c\u3002\u987e\u540d\u601d\u4e49\uff0c\u8fd9\u4e2a\u51fd\u6570\u63a5\u6536\u4e00\u7ec4`SingleCellExperiment`\u5bf9\u8c61\uff0c\u5c06\u6570\u636e\u96c6\u5408\u5e76\uff0c\u5e76\u751f\u6210\u4e00\u4e9b\u6bd4\u8f83\u5b83\u4eec\u7684\u56fe\u8868\u3002\u8ba9\u6211\u4eec\u8fdb\u884c\u4e24\u4e2a\u5c0f\u7684\u6a21\u62df\uff0c\u770b\u770b\u5b83\u4eec\u5982\u4f55\u6bd4\u8f83\u3002<\/p>\n\n\n\n<p>sim1 &lt;- splatSimulate(nGenes = 1000, batchCells = 20, verbose = FALSE)<\/p>\n\n\n\n<p>sim2 &lt;- simpleSimulate(nGenes = 1000, nCells = 20, verbose = FALSE)<\/p>\n\n\n\n<p>comparison &lt;- compareSCEs(list(Splat = sim1, Simple = sim2))<\/p>\n\n\n\n<p>names(comparison)<\/p>\n\n\n\n<p>names(comparison$Plots)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"37\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097319185_3BD9EACF-08F1-44ae-9DEA-E3659A5F1444.png?resize=554%2C37\" alt=\"\" class=\"wp-image-61278\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097319185_3BD9EACF-08F1-44ae-9DEA-E3659A5F1444.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097319185_3BD9EACF-08F1-44ae-9DEA-E3659A5F1444.png?resize=300%2C20 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u8fd4\u56de\u7684\u5217\u8868\u5305\u542b\u4e09\u4e2a\u9879\u76ee\u3002\u524d\u4e24\u4e2a\u662f\u901a\u8fc7\u57fa\u56e0\uff08RowData\uff09\u548c\u901a\u8fc7\u7ec6\u80de\uff08ColData\uff09\u5408\u5e76\u7684\u6570\u636e\u96c6\uff0c\u7b2c\u4e09\u4e2a\u5305\u542b\u4e00\u4e9b\u6bd4\u8f83\u56fe\u8868\uff08\u4f7f\u7528`ggplot2`\u751f\u6210\uff09\uff0c\u4f8b\u5982\uff0c\u4e00\u4e2a\u5c55\u793a<a>\u5747\u503c\u5206\u5e03<\/a>\u7684\u56fe\u8868\uff1a<\/p>\n\n\n\n<p>comparison$Plots$Means<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"296\" height=\"215\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097334348_D6CEB0F9-416C-4c5d-81B9-B40D27D4DDA7.png?resize=296%2C215\" alt=\"\" class=\"wp-image-61279\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u8fd9\u4e9b\u53ea\u662f\u4f60\u53ef\u80fd\u60f3\u8981\u8003\u8651\u7684\u4e00\u4e9b\u56fe\u8868\uff0c\u4f46\u5e94\u8be5\u5f88\u5bb9\u6613\u4f7f\u7528\u8fd4\u56de\u7684\u6570\u636e\u5236\u4f5c\u66f4\u591a\u56fe\u8868\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u7ed8\u5236<a>\u8868\u8fbe\u57fa\u56e0\u6570\u91cf\u4e0e<\/a>\u5e93\u5927\u5c0f\u7684\u5173\u7cfb\u56fe\uff1a<\/p>\n\n\n\n<p>library(&#8220;ggplot2&#8221;)<\/p>\n\n\n\n<p>ggplot(comparison$ColData, aes(x = sum, y = detected, colour = Dataset)) +<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;geom_point()<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"264\" height=\"192\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097347156_547ECADA-6D4A-439d-8271-8D0764DF2F23.png?resize=264%2C192\" alt=\"\" class=\"wp-image-61280\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p><strong>\u6bd4\u8f83\u5dee\u5f02<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6709\u65f6\uff0c\u4e0e\u5176\u76f4\u89c2\u5730\u6bd4\u8f83\u6570\u636e\u96c6\uff0c\u4e0d\u5982\u770b\u770b\u5b83\u4eec\u4e4b\u95f4\u7684\u5dee\u5f02\u3002\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528`diffSCEs`\u51fd\u6570\u6765\u5b9e\u73b0\u8fd9\u4e00\u70b9\u3002\u7c7b\u4f3c\u4e8e`compareSCEs`\uff0c\u8fd9\u4e2a\u51fd\u6570\u4e5f\u63a5\u6536\u4e00\u7ec4`SingleCellExperiment`\u5bf9\u8c61\uff0c\u4f46\u73b0\u5728\u6211\u4eec\u8fd8\u9700\u8981\u6307\u5b9a\u4e00\u4e2a\u4f5c\u4e3a\u53c2\u8003\u7684\u6570\u636e\u96c6\u3002\u8fd4\u56de\u7684\u4e00\u7cfb\u5217\u56fe\u8868\u4e0e\u4e4b\u524d\u7c7b\u4f3c\uff0c\u4f46\u5b83\u4eec\u4e0d\u662f\u5c55\u793a\u6574\u4f53\u5206\u5e03\uff0c\u800c\u662f\u5c55\u793a<a>\u4e0e\u53c2\u8003\u6570\u636e\u96c6\u7684\u5dee\u5f02<\/a>\u3002<\/p>\n\n\n\n<p>difference &lt;- diffSCEs(list(Splat = sim1, Simple = sim2), ref = &#8220;Simple&#8221;)<\/p>\n\n\n\n<p>difference$Plots$Means<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"317\" height=\"230\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097357907_3CC21D45-6DB5-45b6-A255-7F61E1BC0500.png?resize=317%2C230\" alt=\"\" class=\"wp-image-61281\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097357907_3CC21D45-6DB5-45b6-A255-7F61E1BC0500.png?w=317 317w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097357907_3CC21D45-6DB5-45b6-A255-7F61E1BC0500.png?resize=300%2C218 300w\" sizes=\"(max-width: 317px) 100vw, 317px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6211\u4eec\u8fd8\u4f1a\u5f97\u5230\u4e00\u7cfb\u5217<a>\u5206\u4f4d\u6570-\u5206\u4f4d\u6570\u56fe<\/a>\uff0c\u53ef\u4ee5\u7528\u6765\u6bd4\u8f83\u5206\u5e03\u3002<\/p>\n\n\n\n<p>difference$QQPlots$Means<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"324\" height=\"235\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097367580_673C5F6B-C660-43b9-BA77-EFA9DEA4223F.png?resize=324%2C235\" alt=\"\" class=\"wp-image-61282\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097367580_673C5F6B-C660-43b9-BA77-EFA9DEA4223F.png?w=324 324w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097367580_673C5F6B-C660-43b9-BA77-EFA9DEA4223F.png?resize=300%2C218 300w\" sizes=\"(max-width: 324px) 100vw, 324px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p><strong>\u5236\u4f5c\u9762\u677f<\/strong><\/p>\n\n\n\n<p>\u8fd9\u4e9b\u6bd4\u8f83\u4f1a\u751f\u6210\u591a\u4e2a\u56fe\u8868\uff0c\u53ef\u80fd\u4f1a\u8ba9\u4eba\u773c\u82b1\u7f2d\u4e71\u3002\u4e3a\u4e86\u7b80\u5316\u8fd9\u4e2a\u8fc7\u7a0b\uff0c\u6216\u8005\u4e3a\u4e86\u5236\u4f5c\u51fa\u7248\u7269\u4e2d\u7684\u56fe\u8868\uff0c\u4f60\u53ef\u4ee5\u4f7f\u7528`makeCompPanel`\u3001`makeDiffPanel`\u548c`makeOverallPanel`\u51fd\u6570\u3002<\/p>\n\n\n\n<p>\u8fd9\u4e9b\u51fd\u6570\u4f7f\u7528`cowplot`\u5305\u5c06\u56fe\u8868\u5408\u5e76\u6210\u4e00\u4e2a\u9762\u677f\u3002\u9762\u677f\u53ef\u80fd\u4f1a\u5f88\u5927\uff0c\u96be\u4ee5\u67e5\u770b\uff08\u4f8b\u5982\uff0c\u5728RStudio\u7684\u56fe\u8868\u67e5\u770b\u5668\u4e2d\uff09\uff0c\u56e0\u6b64\u6700\u597d\u8f93\u51fa\u9762\u677f\u5e76\u5355\u72ec\u67e5\u770b\u3002\u5e78\u8fd0\u7684\u662f\uff0c`cowplot`\u63d0\u4f9b\u4e86\u4e00\u4e2a\u65b9\u4fbf\u7684\u51fd\u6570\u6765\u4fdd\u5b58\u56fe\u50cf\u3002\u4ee5\u4e0b\u662f\u8f93\u51fa\u6bcf\u4e2a\u9762\u677f\u7684\u4e00\u4e9b\u5efa\u8bae\u53c2\u6570\uff1a<\/p>\n\n\n\n<p>panel &lt;- makeCompPanel(comparison)<\/p>\n\n\n\n<p>cowplot::save_plot(&#8220;comp_panel.png&#8221;, panel, nrow = 4, ncol = 3)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"456\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097379517_FE5F0E80-E29A-4935-A0F4-DC1B41B9A708.png?resize=554%2C456\" alt=\"\" class=\"wp-image-61283\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097379517_FE5F0E80-E29A-4935-A0F4-DC1B41B9A708.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097379517_FE5F0E80-E29A-4935-A0F4-DC1B41B9A708.png?resize=300%2C247 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>panel &lt;- makeDiffPanel(difference)<\/p>\n\n\n\n<p>cowplot::save_plot(&#8220;diff_panel.png&#8221;, panel, nrow = 3, ncol = 5)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"206\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097393306_64B04F6B-8879-4d76-8B49-B33BEC840847.png?resize=554%2C206\" alt=\"\" class=\"wp-image-61284\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097393306_64B04F6B-8879-4d76-8B49-B33BEC840847.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097393306_64B04F6B-8879-4d76-8B49-B33BEC840847.png?resize=300%2C112 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>panel &lt;- makeOverallPanel(comparison, difference)<\/p>\n\n\n\n<p>cowplot::save_plot(&#8220;overall_panel.png&#8221;, panel, ncol = 4, nrow = 7)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"599\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097409121_7A33DEE1-CCD6-48e8-BB2B-4865223CE605.png?resize=554%2C599\" alt=\"\" class=\"wp-image-61285\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097409121_7A33DEE1-CCD6-48e8-BB2B-4865223CE605.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730097409121_7A33DEE1-CCD6-48e8-BB2B-4865223CE605.png?resize=277%2C300 277w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u901a\u8fc7\u8fd9\u4e9b\u51fd\u6570\uff0c\u6211\u4eec\u53ef\u4ee5\u66f4\u76f4\u89c2\u5730\u6bd4\u8f83\u4e0d\u540c\u6a21\u62df\u6570\u636e\u96c6\u4e4b\u95f4\u7684\u5dee\u5f02\uff0c\u5e76\u4e14\u80fd\u591f\u5c06\u8fd9\u4e9b\u6bd4\u8f83\u6574\u5408\u6210\u4e00\u4e2a\u6613\u4e8e\u67e5\u770b\u548c\u7406\u89e3\u7684\u9762\u677f\u3002\u8fd9\u6837\uff0c\u65e0\u8bba\u662f\u5728\u7814\u7a76\u4e2d\u8fd8\u662f\u5728\u51c6\u5907\u53d1\u8868\u7684\u8bba\u6587\u4e2d\uff0c\u6211\u4eec\u90fd\u80fd\u591f\u66f4\u6709\u6548\u5730\u5c55\u793a\u6211\u4eec\u7684\u53d1\u73b0\u3002<\/p>\n\n\n\n<p>\u901a\u8fc7\u4f7f\u7528Splatter\u5305\u8fdb\u884c\u6a21\u62df\uff0c\u6211\u4eec\u80fd\u591f\u9ad8\u6548\u5730\u751f\u6210\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6570\u636e\uff0c\u4e3a\u7814\u7a76\u63d0\u4f9b\u4e86\u5f3a\u6709\u529b\u7684\u652f\u6301\u3002\u8fd9\u4e0d\u4ec5\u5e2e\u52a9\u6211\u4eec\u7406\u89e3\u57fa\u56e0\u8868\u8fbe\u7684\u590d\u6742\u6027\uff0c\u4e5f\u4e3a\u672a\u6765\u7684\u751f\u7269\u533b\u5b66\u7814\u7a76\u5960\u5b9a\u4e86\u57fa\u7840\u3002<strong>\u5982\u679c\u4f60\u5bf9\u5982\u4f55\u5e94\u7528\u8fd9\u4e2a\u5f3a\u5927\u7684\u5de5\u5177\u6709\u4efb\u4f55\u7591\u95ee\uff0c\u8bb0\u5f97\u627e\u5c0f\u5e08\u59b9\uff0c\u8ba9\u6211\u4eec\u4e00\u8d77\u63a2\u7d22\u57fa\u56e0\u7ec4\u7684\u5965\u79d8\uff01<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u65e0\u8bba\u4f60\u662f\u5728\u4f18\u5316\u4ee3\u7801\uff0c\u8fd8\u662f\u5728\u4e91\u7aef\u8fdb\u884c\u4fbf\u6377\u7684\u5206\u6790\uff0c\u4e91\u751f\u4fe1\u795e\u5668\u90fd\u80fd\u4e3a\u4f60\u63d0\u4f9b\u5f3a\u5927\u7684\u652f\u6301\u3002<strong>\u6b22\u8fce\u8bd5\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u795e\u5668\uff0c\u53ea\u9700\u4e00\u952e\u4e0a\u4f20\u6570\u636e\uff0c\u60f3\u8981\u7684\u56fe\u5c31\u80fd\u8f7b\u677eget~<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/strong><a href=\"http:\/\/www.biocloudservice.com\/home.html\"><strong>http:\/\/www.biocloudservice.com\/home.html<\/strong><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u563f\uff0c\u79d1\u7814\u5c0f\u4f19\u4f34\u4eec\uff0c\u5c0f\u5e08\u59b9\u6211\u53c8\u6765\u5566\uff01\u4eca\u5929\uff0c\u6211\u8981\u7ed9\u5927\u5bb6\u5e26\u6765\u4e00\u4e2a\u8d85\u7ea7\u5b9e\u7528\u7684\u751f\u7269\u4fe1\u606f\u5b66\u5de5\u5177\u2014\u2014Splatter\u5305\u3002\u5728\u8fd9 [&hellip;]<\/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\/61253"}],"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=61253"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61253\/revisions"}],"predecessor-version":[{"id":61286,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61253\/revisions\/61286"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61253"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61253"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61253"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}