{"id":29770,"date":"2024-02-26T17:38:16","date_gmt":"2024-02-26T09:38:16","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29770"},"modified":"2024-02-26T17:38:18","modified_gmt":"2024-02-26T09:38:18","slug":"%e7%94%9f%e4%bf%a1%e5%ad%a6%e4%b9%a0%e4%b9%8bscater%e5%8c%85%e7%9a%84%e5%ae%89%e8%a3%85%e4%b8%8e%e7%ae%80%e5%8d%95%e5%ba%94%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29770","title":{"rendered":"\u751f\u4fe1\u5b66\u4e60\u4e4bscater\u5305\u7684\u5b89\u88c5\u4e0e\u7b80\u5355\u5e94\u7528"},"content":{"rendered":"<p><strong>\u751f\u4fe1\u5b66\u4e60\u4e4bscater\u5305\u7684\u5b89\u88c5\u4e0e\u7b80\u5355\u5e94\u7528<\/strong><\/p>\n<p><strong>\u4ec0\u4e48\u662fscater?<\/strong><\/p>\n<p>\u200b\u5c0f\u679c\u4eca\u5929\u5b66\u4e60\u7684R\u5305\u662fscater\uff0c\u90a3\u4e48\u9996\u5148\u6765\u7b80\u5355\u4e86\u89e3\u4e00\u4e0bscater\u5305\u7684\u57fa\u672c\u6982\u5ff5\u5427\uff01<\/p>\n<p>scater\u662f\u4e00\u4e2a\u7528\u6765\u5bf9\u5355\u7ec6\u80deRNA-seq\u6570\u636e\u8fdb\u884c\u9884\u5904\u7406\u3001\u8d28\u91cf\u63a7\u5236\u3001\u89c4\u8303\u5316\u548c\u53ef\u89c6\u5316\u7684R\u5de5\u5177\u5305\u3002\u9996\u5148\uff0c\u8be5R\u5de5\u5177\u5305\u53ef\u4ee5\u5bf9\u8f93\u5165\u7684\u539f\u59cb\u6d4b\u5e8f\u6570\u636e\u5904\u7406\u4e3a\u9ad8\u8d28\u91cf\u7684\u8868\u8fbe\u6570\u636e\u96c6\uff0c\u4e5f\u63d0\u4f9b\u4e86\u4e0d\u540c\u79cd\u7c7b\u7684\u7ed8\u56fe\u6a21\u5757\u4ee5\u5b9e\u73b0\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u4e0d\u540c\u7ef4\u5ea6\u65b9\u9762\u7684\u53ef\u89c6\u5316\u5de5\u4f5c\u3002\u90a3\u63a5\u4e0b\u6765\u5927\u5bb6\u5c31\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5982\u4f55\u5b89\u88c5scater\u5305\u5427\uff01<\/p>\n<p><strong>scater\u7684\u5b89\u88c5<\/strong><\/p>\n<p>\u200b \u56e0\u4e3ascater\u7684\u5b89\u88c5\u662f\u57fa\u4e8egithub\u6765\u5b89\u88c5\u7684\uff0c\u6240\u4ee5\u6ca1\u6709\u5b89\u88c5devtools\u8f6f\u4ef6\u5305\u7684\u540c\u5b66\u8981\u5148\u5b89\u88c5\u597ddevtools\u5de5\u5177\u5305~<\/p>\n<p>if(!require(devtools))<br \/>\ninstall.packages(&#8220;devtools&#8221;)<br \/>\nif(!require(scater))<br \/>\ndevtools::install_github(&#8220;davismcc\/scater&#8221;, build_vignettes = TRUE)<\/p>\n<ul>\n<li><strong>scater\u8f6f\u4ef6\u5305\u5b89\u88c5\u65f6\u53ef\u80fd\u4f1a\u51fa\u73b0\u7684\u9519\u8bef<\/strong><\/li>\n<\/ul>\n<p>\u4e0b\u8f7d\u7684\u65f6\u5019\u4f60\u4e5f\u8bb8\u56de\u6536\u5230\u62a5\u9519\u4fe1\u606f\uff0c\u8fd9\u662f\u600e\u4e48\u56de\u4e8b\u5462\uff1f\u5728\u4e0b\u8f7d\u7684\u8fc7\u7a0b\u4e2d\u5c0f\u679c\u4e5f\u9047\u5230\u4e86\u540c\u6837\u7684\u95ee\u9898\uff01\u8ba9\u6211\u4eec\u6765\u4e00\u8d77\u770b\u4e00\u4e0b\u5427\uff01<\/p>\n<p>\u54c8\u54c8\u54c8\uff01\u539f\u6765\u662f\u662f\u7531\u4e8escater\u5de5\u5177\u5305\u7684\u5b89\u88c5\u8fd8\u4f9d\u8d56\u4e86\u2018BiocStyle\u2019\u8f6f\u4ef6\u5305\uff0c\u5982\u679c\u6ca1\u6709\u63d0\u524d\u5b89\u88c5\uff0c\u5219\u4f1a\u51fa\u73b0\u4ee5\u4e0b\u9519\u8bef\u4fe1\u606f\uff1a<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"294\" class=\"wp-image-29771\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-72.png?resize=640%2C294\" alt=\"\u6587\u672c, \u7535\u5b50\u90ae\u4ef6\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-72.png?w=1033 1033w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-72.png?resize=300%2C138 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-72.png?resize=1024%2C470 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-72.png?resize=768%2C352 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-72.png?resize=600%2C275 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u4e3a\u4e86\u89e3\u51b3\u8fd9\u4e00\u95ee\u9898\uff0c\u6211\u4eec\u5148\u5b89\u88c5 BiocStyle\u8f6f\u4ef6\u5305\uff0c\u6211\u4eec\u501f\u52a9Bioconductor\u6765\u5b89\u88c5\uff1a<br \/>\nBiocManager::install(c(&#8220;BiocStyle&#8221;))<\/p>\n<p>\u597d\u4e86\uff0c\u4e0b\u9762\u6211\u4eec\u5c31\u53ef\u4ee5\u7ee7\u7eed\u5b89\u88c5scater\u8f6f\u4ef6\u5305\uff1a<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"218\" class=\"wp-image-29772\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-73.png?resize=640%2C218\" alt=\"\u56fe\u5f62\u7528\u6237\u754c\u9762, \u6587\u672c, \u5e94\u7528\u7a0b\u5e8f, \u7535\u5b50\u90ae\u4ef6\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-73.png?w=1247 1247w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-73.png?resize=300%2C102 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-73.png?resize=1024%2C349 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-73.png?resize=768%2C262 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-73.png?resize=600%2C204 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p><strong>scater\u5305\u7684\u4f7f\u7528<\/strong><\/p>\n<ul>\n<li><strong>\u51c6\u5907\u6570\u636e<\/strong><\/li>\n<\/ul>\n<p>\u54fc\u54fc\uff0c\u5c0f\u679c\u63d0\u9192\uff1a\u6211\u4eec\u7684\u6570\u636e\u57fa\u4e8eBiocStyle\u548cscRNAseq\u8fd9\u4e24\u4e2a\u5305\u6765\u51c6\u5907\u54e6\uff01<\/p>\n<p>library(BiocStyle)<br \/>\nlibrary(scRNAseq)<br \/>\nset.seed(10918)<br \/>\ndata &lt;- ZeiselBrainData()<br \/>\ndata<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"171\" class=\"wp-image-29773\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-74.png?resize=640%2C171\" alt=\"\u56fe\u5f62\u7528\u6237\u754c\u9762, \u6587\u672c, \u5e94\u7528\u7a0b\u5e8f\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-74.png?w=1297 1297w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-74.png?resize=300%2C80 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-74.png?resize=1024%2C274 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-74.png?resize=768%2C205 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-74.png?resize=600%2C161 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u4ece\u8f93\u51fa\u4fe1\u606f\u4e2d\u53ef\u4ee5\u770b\u51fa\u6570\u636e\u7684\u7ef4\u5ea6\u662f20006\u884c\u548c3005\u5217\u3002<\/p>\n<ul>\n<li><strong>\u6570\u636e\u8d28\u63a7<\/strong><\/li>\n<\/ul>\n<p>\u597d\u5566\uff01\u6570\u636e\u51c6\u5907\u597d\u540e\u6211\u4eec\u5c31\u8981\u8fdb\u884c\u6211\u4eec\u7ecf\u5e38\u4f1a\u8fdb\u884c\u7684\u6570\u636e\u8d28\u63a7\u5de5\u4f5c\u5566~<\/p>\n<p>\u73b0\u5728\u5c0f\u679c\u8981\u57fa\u4e8e\u51c6\u5907\u597d\u7684\u6570\u636e\u8fdb\u884c\u8d28\u63a7\uff0c\u53bb\u6389\u5176\u4e2d\u7684\u7ebf\u7c92\u4f53\u57fa\u56e0\uff0c\u4e5f\u5c31\u662f\u4ee5\u201cmt\u201d\u5f00\u5934\u7684\u57fa\u56e0\u54e6\u3002<\/p>\n<p>library(scater)<br \/>\ndata &lt;- addPerCellQC(data,<br \/>\nsubsets=list(Mito=grep(&#8220;mt-&#8220;, rownames(data))))<\/p>\n<ul>\n<li><strong>\u7ec6\u80de\u4fe1\u606f\u53ef\u89c6\u5316<\/strong><\/li>\n<\/ul>\n<p>\u5c06\u6211\u4eec\u4e0a\u9762\u8d28\u63a7\u540e\u7684\u6570\u636e\u63d0\u53d6tissue\u548cclass\uff1a<\/p>\n<p>tp = as.data.frame(data@colData)<br \/>\ntable(tp$tissue)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"523\" height=\"103\" class=\"wp-image-29774\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-75.png?resize=523%2C103\" alt=\"\u56fe\u7247\u5305\u542b \u56fe\u5f62\u7528\u6237\u754c\u9762\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-75.png?w=523 523w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-75.png?resize=300%2C59 300w\" sizes=\"(max-width: 523px) 100vw, 523px\" data-recalc-dims=\"1\" \/><\/p>\n<p>table(tp$level1class)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"249\" class=\"wp-image-29775\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-76.png?resize=640%2C249\" alt=\"\u8868\u683c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-76.png?w=682 682w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-76.png?resize=300%2C117 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-76.png?resize=600%2C233 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>table(tp$sex)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"276\" height=\"100\" class=\"wp-image-29776\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-77.png?resize=276%2C100\" alt=\"\u56fe\u7247\u5305\u542b \u6587\u672c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u4ee5\u4e0a\u9762\u7684\u4fe1\u606f\u5217\u4e3a\u57fa\u7840\uff0c\u63a5\u4e0b\u6765\u7528scater\u7684\u53ef\u89c6\u5316\u529f\u80fd\u5c55\u793acount\u6570\u548c\u68c0\u6d4b\u5230\u57fa\u56e0\u6570\u7684\u5173\u7cfb\uff0c\u84dd\u8272\u548c\u6a59\u8272\u5206\u522b\u4ee3\u8868tissue\u4e0b\u7684ca1hippocampus\u548csscortex\u4fe1\u606f\u5217\u3002<\/p>\n<p>plotColData(data, x = &#8220;sum&#8221;, y=&#8221;detected&#8221;, colour_by=&#8221;tissue&#8221;)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"395\" class=\"wp-image-29777\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29770-7.png?resize=640%2C395\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29770-7.png?w=1892 1892w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29770-7.png?resize=300%2C185 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29770-7.png?resize=1024%2C632 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29770-7.png?resize=768%2C474 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29770-7.png?resize=1536%2C948 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29770-7.png?resize=600%2C370 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29770-7.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>D=====(\uffe3\u25bd\uffe3*)b\u4eca\u5929\u7684\u5b66\u4e60\u8bfe\u7a0b\u5c31\u5230\u8fd9\u91cc\u54e6~~<\/p>\n<p>\u4ee5\u4e0a\u5c31\u662f\u5c0f\u679c\u5bf9scater\u5305\u7684\u7b80\u5355\u4ecb\u7ecd\uff0c\u4f60\u5b66\u4f1a\u5b83\u7684\u57fa\u672c\u64cd\u4f5c\u4e86\u561b\uff1fscater\u4e0b\u8fd8\u6709\u5f88\u591a\u4e2d\u53ef\u89c6\u5316\u7684\u9886\u57df\u7b49\u7740\u6211\u4eec\u63a2\u7d22\uff0c\u8ba9\u6211\u4eec\u7ee7\u7eed\u7814\u7a76\u4e0b\u53bb\u5427\uff01\u4eca\u5929\u7684\u5c0f\u77e5\u8bc6\u5bf9\u4f60\u7684\u5b66\u4e60\u662f\u5426\u6709\u7528\u634f\uff1f\u5982\u679c\u6709\u7528\u8bb0\u5f97\u7ee7\u7eed\u5173\u6ce8\u5c0f\u679c\u5965~~<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u751f\u4fe1\u5b66\u4e60\u4e4bscater\u5305\u7684\u5b89\u88c5\u4e0e\u7b80\u5355\u5e94\u7528 \u4ec0\u4e48\u662fscater? \u200b\u5c0f\u679c\u4eca\u5929\u5b66\u4e60\u7684R\u5305\u662fscater\uff0c\u90a3\u4e48\u9996\u5148\u6765 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29770"}],"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=29770"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29770\/revisions"}],"predecessor-version":[{"id":29778,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29770\/revisions\/29778"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29770"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29770"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29770"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}