{"id":61184,"date":"2024-10-17T14:12:29","date_gmt":"2024-10-17T06:12:29","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61184"},"modified":"2024-10-17T14:12:29","modified_gmt":"2024-10-17T06:12:29","slug":"%e7%ae%80%e5%8d%95%ef%bc%81%e4%b8%80%e8%a1%8c%e4%bb%a3%e7%a0%81%e5%ae%8c%e6%88%90rna-seq%e4%b8%8b%e6%b8%b8%e5%88%86%e6%9e%90%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61184","title":{"rendered":"\u7b80\u5355\uff01\u4e00\u884c\u4ee3\u7801\u5b8c\u6210RNA-seq\u4e0b\u6e38\u5206\u6790\uff01"},"content":{"rendered":"\n<p><\/p>\n\n\n\n<p>Hello! \u4eca\u5929\u6211\u5f88\u9ad8\u5174\u5730\u5411\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u4ee4\u4eba\u632f\u594b\u7684R\u5305\u2014\u2014RNAseqStat2\u3002\u8fd9\u6b3e\u5de5\u5177\u7b80\u76f4\u662f\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u7684\u5229\u5668\uff0c\u53ea\u9700\u4e00\u884c\u547d\u4ee4\uff0c\u4fbf\u80fd\u8f7b\u677e\u5e94\u5bf9RNA-seq\u7684\u4e0b\u6e38\u5206\u6790\u6311\u6218\u3002\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5c06\u5e26\u4f60\u4eec\u8fdb\u5165RNAseqStat2\u7684\u5b9e\u6218\u5e94\u7528\uff0c\u5206\u5206\u949f\u6559\u4f1a\u4f60\u4eec\u5982\u4f55\u5f97\u5230\u6f02\u4eae\u7684\u7ed3\u679c\u56fe\uff01<strong>\u4f5c\u4e3a\u5728\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\u6478\u722c\u6eda\u6253\u591a\u5e74\u7684\u6211\uff0c\u975e\u5e38\u4e50\u610f\u4e0e\u5927\u5bb6\u5206\u4eab\u6211\u7684\u7ecf\u9a8c\u548c\u77e5\u8bc6\u3002\u82e5\u60a8\u5728\u8fdb\u884c\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u65f6\u9047\u5230\u96be\u9898\uff0c\u968f\u65f6\u6b22\u8fce\u5411\u6211\u5bfb\u6c42\u5e2e\u52a9\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u5982\u4f55\u4f7f\u7528\u4e00\u884c\u4ee3\u7801\u4fbf\u6377\u5730\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u548c\u5bcc\u96c6\u5206\u6790\u5462\uff1f\u522b\u6025\uff0c\u4eca\u5929\u5c0f\u679c\u5c31\u7528\u4e00\u6bb5\u4ee3\u7801\u6765\u793a\u8303\uff0c\u624b\u628a\u624b\u6559\u4f60\u4eec\u5982\u4f55\u9a7e\u9a6dRNAseqStat2\uff0c\u8ba9\u4f60\u4eec\u5728RNA-seq\u6570\u636e\u5206\u6790\u7684\u5f81\u9014\u4e0a\uff0c\u8f7b\u677e\u6109\u5feb\u5730\u6536\u83b7\u90a3\u4e9b\u4ee4\u4eba\u60ca\u8273\u7684\u53ef\u89c6\u5316\u6210\u679c\uff01<\/p>\n\n\n\n<p><strong>\u5728\u6211\u4eec\u6df1\u5165\u63a2\u7d22R\u5305\u7684\u65e0\u9650\u53ef\u80fd\u65f6\uff0c\u5c0f\u679c\u6ce8\u610f\u5230\uff0c\u67d0\u4e9b\u5f3a\u5927\u7684R\u5305\u5728\u8fd0\u884c\u65f6\u53ef\u80fd\u4f1a\u5bf9\u60a8\u7684\u8ba1\u7b97\u673a\u5185\u5b58\u63d0\u51fa\u8f83\u9ad8\u7684\u8981\u6c42\u3002\u5c0f\u679c\u5728\u8fd9\u91cc\u4e3a\u60a8\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u6027\u4ef7\u6bd4\u6781\u9ad8\u7684\u670d\u52a1\u5668\u79df\u8d41\u9009\u9879\uff0c\u65e8\u5728\u6ee1\u8db3\u60a8\u4ece\u8f7b\u91cf\u7ea7\u5230\u91cd\u91cf\u7ea7\u7684\u6570\u636e\u5206\u6790\u9700\u6c42\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<ul>\n<li><strong>\u4e00\uff1a\u5b89\u88c5\u4ee5\u53ca\u52a0\u8f7dR\u5305<\/strong><strong><\/strong><\/li>\n<\/ul>\n\n\n\n<p>library(devtools)<\/p>\n\n\n\n<p>devtools::install_github(&#8220;xiayh17\/RNAseqStat2&#8221;)<\/p>\n\n\n\n<ul>\n<li><strong>\u4e8c\uff1a\u6a21\u5f0f\u751f\u7269\uff0c\u4e00\u6b65\u5b8c\u6210\u5206\u6790<\/strong><strong><\/strong><\/li>\n<\/ul>\n\n\n\n<p>\u6a21\u5f0f\u751f\u7269\u53ea\u9700\u8981\u6309\u7167\u793a\u4f8b\u6570\u636e\u6574\u7406\u6587\u4ef6\u5373\u53ef\uff0c\u4e0b\u8f7d\u5bf9\u5e94\u7684OrgDB\u5305\uff0c\u4e00\u884c\u547d\u4ee4\u5373\u53ef\u51fa\u56fe\uff0c\u975e\u5e38\u7684\u7b80\u5355\u3002\u5982\u679c\u662fHuman, Mouse,Rat \u4e4b\u4e00\uff0c\u6574\u4f53\u5206\u6790\u975e\u5e38\u7b80\u5355\uff0c\u77ed\u77ed\u51e0\u884c\u5373\u53ef\u5b8c\u6210\u5168\u90e8\u5206\u6790\uff0c\u4ee5airway\u7684\u6570\u636e\u4e3a\u4f8b\uff08R\u4e2d\u7684airway\u6570\u636e\u96c6\u662f\u4e00\u4e2aRNA\u6d4b\u5e8f\u6570\u636e\u96c6\uff0c\u5b83\u5305\u542b\u4e86\u56db\u4e2a\u4eba\u7c7b\u6c14\u9053\u5e73\u6ed1\u808c\u7ec6\u80de\u7cfb\uff08airway smooth muscle cell lines\uff09\u5728\u63a5\u53d7\u5730\u585e\u7c73\u677e\uff08dexamethasone\uff0c\u4e00\u79cd\u7cd6\u76ae\u8d28\u6fc0\u7d20\uff09\u5904\u7406\u540e\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002<\/p>\n\n\n\n<p>library(RNAseqStat2)<\/p>\n\n\n\n<p>library(airway)<\/p>\n\n\n\n<p>data(&#8220;airway&#8221;)<\/p>\n\n\n\n<p>row_counts &lt;- as.data.frame(assay(airway))<\/p>\n\n\n\n<p>group_list &lt;- as.character(colData(airway)$dex)<\/p>\n\n\n\n<p>data_i &lt;- Create_DEGContainer(species = &#8220;Human&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dataType = &#8220;Counts&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;idType = &#8220;ENSEMBL&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;expMatrix = row_counts,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;groupInfo = group_list,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;caseGroup = &#8220;trt&#8221;)<\/p>\n\n\n\n<p># \u4e00\u6b65\u8fd0\u884c<\/p>\n\n\n\n<p>data_o &lt;- runALL(object = data_i,dir = &#8220;output_test&#8221;)<\/p>\n\n\n\n<p>\u5728\u8fd9\u91cc\u5c0f\u679c\u63d0\u9192\u5927\u5bb6\uff0c\u5982\u679c\u662f\u5176\u4ed6\u7269\u79cd\uff0c\u9700\u8981\u6839\u636e\u79d1\u5b66\u95ee\u9898\u800c\u8bbe\u7f6e\u53c2\u6570\uff0c\u4e0b\u8f7d\u5bf9\u5e94\u7684OrgDB\u5305\u3002<\/p>\n\n\n\n<p>data_i &lt;- Create_DEGContainer(species = &#8220;pig&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dataType = &#8220;Counts&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;idType = &#8220;SYMBOL&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;expMatrix = row_counts,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;groupInfo = group_list,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;caseGroup = &#8220;NBW&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;OrgDb=&#8221;org.Ss.eg.db&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;organism=&#8221;ssc&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;msi_species=&#8221;Sus scrofa&#8221;)<\/p>\n\n\n\n<ul>\n<li><strong>\u4e09\uff1a\u975e\u6a21\u5f0f\u7269\u79cd\u6784\u5efa\u5bf9\u8c61<\/strong><strong><\/strong><\/li>\n<\/ul>\n\n\n\n<p>\u5c0f\u4f17\u7684\u975e\u6a21\u5f0f\u751f\u7269\u751a\u81f3\u90fd\u6ca1\u6709\u5408\u9002\u7684Org.Db\u6570\u636e\u5e93\u3002\u8fd9\u4e2a\u65f6\u5019\u5c31\u9700\u8981\u81ea\u5df1\u51c6\u5907\u4e00\u4e9b\u6587\u4ef6\uff0c\u5305\u62ec\u6ce8\u91ca\u6587\u4ef6\u7b49\u3002\u5c0f\u679c\u8fd9\u8fb9\u6765\u8be6\u7ec6\u8bb2\u89e3\u4e00\u4e0b\u3002<\/p>\n\n\n\n<p>\u9996\u5148\u9700\u8981\u51c6\u59075\u4e2a\u521d\u59cb\u6587\u4ef6\uff0c\u5305\u62ec\u539f\u59cb\u8868\u8fbe\u91cf\u77e9\u9635\u548c\u6ce8\u91ca\u6587\u4ef6\u3002\u5bf9\u4e8e\u975e\u6a21\u5f0f\u690d\u7269\uff0c\u83b7\u53d6GO\uff08Gene Ontology\uff09\u548cKEGG\uff08Kyoto Encyclopedia of Genes and Genomes\uff09\u6ce8\u91ca\u6587\u4ef6\u7684\u65b9\u6cd5\u901a\u5e38\u6d89\u53ca\u4ee5\u4e0b\u51e0\u4e2a\u65b9\u6cd5\uff1a\u4e00\u3001\u4f7f\u7528EGGNOG-Mapper\u8fdb\u884c\u6ce8\u91ca\uff1a\u5bf9\u4e8e\u975e\u6a21\u5f0f\u7269\u79cd\uff0c\u53ef\u4ee5\u4f7f\u7528EGGNOG-Mapper\u6765\u5feb\u901f\u8fdb\u884cGO\u6216KEGG\u6ce8\u91ca\u3002\u6ce8\u91ca\u7ed3\u679c\u6587\u4ef6\u4e2d\u5c06\u5305\u542b\u5e8f\u5217\u6620\u5c04\u4e0a\u7684GO\u53f7\u6216KO\u53f7\u3002\u4e8c\u3001\u53ef\u4ee5\u5c06\u86cb\u767d\u6587\u4ef6\u4e0a\u4f20\u5230KEGG\u6ce8\u91ca\u7684\u7f51\u7ad9\uff08<a href=\"https:\/\/www.genome.jp\/tools\/kofamkoala\/\"><u>https:\/\/www.genome.jp\/tools\/kofamkoala<\/u><\/a>\uff09\u4e2d\u8fdb\u884c\u6ce8\u91ca\u3002\u521d\u59cb\u6587\u4ef6\u5982\u4e0b\uff1a<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"760\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144738227_6E3ACB70-A461-4a73-BD65-FABD159A253A.png?resize=554%2C760\" alt=\"\" class=\"wp-image-61185\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144738227_6E3ACB70-A461-4a73-BD65-FABD159A253A.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144738227_6E3ACB70-A461-4a73-BD65-FABD159A253A.png?resize=219%2C300 219w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"584\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144747051_9627C999-B83F-4fd3-9BB2-AC54BEB580A2.png?resize=554%2C584\" alt=\"\" class=\"wp-image-61186\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144747051_9627C999-B83F-4fd3-9BB2-AC54BEB580A2.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144747051_9627C999-B83F-4fd3-9BB2-AC54BEB580A2.png?resize=285%2C300 285w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"267\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144757278_C00362A3-D9C8-440b-9214-1262D5675197.png?resize=554%2C267\" alt=\"\" class=\"wp-image-61187\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144757278_C00362A3-D9C8-440b-9214-1262D5675197.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144757278_C00362A3-D9C8-440b-9214-1262D5675197.png?resize=300%2C145 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"478\" height=\"870\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144767596_A9B3AEBF-7295-4fc0-90D1-112129B6630E.png?resize=478%2C870\" alt=\"\" class=\"wp-image-61188\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144767596_A9B3AEBF-7295-4fc0-90D1-112129B6630E.png?w=478 478w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144767596_A9B3AEBF-7295-4fc0-90D1-112129B6630E.png?resize=165%2C300 165w\" sizes=\"(max-width: 478px) 100vw, 478px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"383\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144778026_BFDE9138-5BE2-4ec5-A6CB-8A8A21C9A7F9.png?resize=554%2C383\" alt=\"\" class=\"wp-image-61189\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144778026_BFDE9138-5BE2-4ec5-A6CB-8A8A21C9A7F9.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144778026_BFDE9138-5BE2-4ec5-A6CB-8A8A21C9A7F9.png?resize=300%2C207 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u51c6\u5907\u597d\u6587\u4ef6\u5373\u53ef\u5f00\u59cb\u6784\u5efa\u5bf9\u8c61<\/p>\n\n\n\n<p># \u52a0\u8f7dRNAseqStat2\u5305\uff0c\u7528\u4e8eRNA-seq\u6570\u636e\u5206\u6790<\/p>\n\n\n\n<p>library(RNAseqStat2)<\/p>\n\n\n\n<p># \u52a0\u8f7ddplyr\u5305\uff0c\u7528\u4e8e\u6570\u636e\u64cd\u4f5c\u548c\u5904\u7406<\/p>\n\n\n\n<p>library(dplyr)<\/p>\n\n\n\n<p># \u8bfb\u53d6\u884c\u8ba1\u6570\u6570\u636e\uff0c\u8fd9\u91cc\u5047\u8bbe\u6570\u636e\u662f\u4ee5\u7a7a\u683c\u5206\u9694\u7684\uff0c\u5e76\u4e14\u7b2c\u4e00\u884c\u5305\u542b\u5217\u540d\uff0c\u884c\u540d\u4e3a\u6570\u636e\u7684\u7b2c\u4e00\u5217<\/p>\n\n\n\n<p># \u8bf7\u6839\u636e\u5b9e\u9645\u6587\u4ef6\u683c\u5f0f\u8c03\u6574sep\u53c2\u6570\uff08\u4f8b\u5982\uff0c\u5982\u679c\u662f\u9017\u53f7\u5206\u9694\uff0c\u4f7f\u7528&#8221;,&#8221;\uff09<\/p>\n\n\n\n<p>row_counts &lt;- read.delim(&#8220;SRD.txt&#8221;, header=TRUE, sep = &#8221; &#8221; , row.names=1)<\/p>\n\n\n\n<p># \u5b9a\u4e49\u5206\u7ec4\u5217\u8868\uff0c\u6bcf\u4e2a\u5143\u7d20\u5bf9\u5e94\u4e00\u4e2a\u6837\u672c\u7684\u5206\u7ec4<\/p>\n\n\n\n<p># \u8fd9\u91cc\u7684\u5206\u7ec4\u540d\u79f0\u662f\u793a\u4f8b\uff0c\u5e94\u6839\u636e\u5b9e\u9645\u6837\u672c\u5206\u7ec4\u8fdb\u884c\u4fee\u6539<\/p>\n\n\n\n<p>group_list &lt;- c(&#8220;SRRR&#8221;,&#8221;SRRR&#8221;,&#8221;SRRR&#8221;,&#8221;SDDD&#8221;,&#8221;SDDD&#8221;,&#8221;SDDD&#8221;)<\/p>\n\n\n\n<p># \u8bfb\u53d6\u57fa\u56e0\u7684GO\u6ce8\u91ca\u6587\u4ef6\uff0c\u8fd9\u91cc\u5047\u8bbe\u6587\u4ef6\u662f\u4ee5\u5236\u8868\u7b26\u5206\u9694\u7684\uff0c\u6ca1\u6709\u5217\u540d\uff0c\u4e0d\u68c0\u67e5\u57fa\u56e0\u540d\u7684\u6709\u6548\u6027<\/p>\n\n\n\n<p># \u8bf7\u6839\u636e\u5b9e\u9645\u6587\u4ef6\u683c\u5f0f\u8c03\u6574sep\u53c2\u6570\u548cheader\u53c2\u6570<\/p>\n\n\n\n<p>GO_anno &lt;- read.csv(&#8220;gene_go_annotation_from_ipr_nr.tab&#8221;, sep = &#8220;\\t&#8221;, header = FALSE, check.names = FALSE)<\/p>\n\n\n\n<p># \u8bfb\u53d6GO\u672f\u8bed\u7684\u63cf\u8ff0\u6587\u4ef6\uff0c\u540c\u6837\u5047\u8bbe\u6ca1\u6709\u5217\u540d\uff0c\u4e0d\u68c0\u67e5\u672f\u8bed\u540d\u7684\u6709\u6548\u6027<\/p>\n\n\n\n<p>GO_description &lt;- read.csv(&#8220;go_term.list&#8221;, sep = &#8220;\\t&#8221;, header = FALSE, check.names = FALSE)<\/p>\n\n\n\n<p># \u8bfb\u53d6\u57fa\u56e0\u7684KEGG\u6ce8\u91ca\u6587\u4ef6\uff0c\u5047\u8bbe\u6587\u4ef6\u683c\u5f0f\u4e0eGO\u6ce8\u91ca\u6587\u4ef6\u76f8\u540c<\/p>\n\n\n\n<p>KEGG_anno &lt;- read.csv(&#8220;kegg_gene.txt&#8221;, sep = &#8220;\\t&#8221;, header = FALSE, check.names = FALSE)<\/p>\n\n\n\n<p># \u8bfb\u53d6KEGG\u8def\u5f84\u7684\u63cf\u8ff0\u6587\u4ef6\uff0c\u5047\u8bbe\u6587\u4ef6\u683c\u5f0f\u4e0eGO\u63cf\u8ff0\u6587\u4ef6\u76f8\u540c<\/p>\n\n\n\n<p>KEGG_description &lt;- read.csv(&#8220;kegg_description.txt&#8221;, sep = &#8220;\\t&#8221;, check.names = FALSE, header = FALSE)<\/p>\n\n\n\n<p>#\u6784\u5efa\u5bf9\u8c61<\/p>\n\n\n\n<p>data_i &lt;- Create_DEGContainer(expMatrix = row_counts,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;groupInfo = group_list,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;caseGroup = &#8220;SDDD&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;species = &#8220;unknow&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GOTERM2GENE = GO_anno,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GOTERM2NAME = GO_description,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;KEGGTERM2GENE = KEGG_anno,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;KEGGTERM2NAME = KEGG_description)<\/p>\n\n\n\n<p>#\u4e00\u6b65\u6cd5\u5b8c\u6210\u6570\u636e\u5206\u6790<\/p>\n\n\n\n<p>data_o &lt;- runALL(object = data_i,dir = &#8220;output&#8221;)<\/p>\n\n\n\n<p>#\u8fd9\u91cc\u5c0f\u679c\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e0b\u51fd\u6570\u5305\u542b\u7684\u53c2\u6570\uff1a<\/p>\n\n\n\n<p>expMatrix \u5904\u7406\u597d\u7684\u8868\u8fbe\u77e9\u9635<\/p>\n\n\n\n<p>species \u7269\u79cd\u540d \u6bd4\u5982 Human Mouse Rat \u6216\u8005\u5176\u4ed6<\/p>\n\n\n\n<p>groupInfo \u5206\u7ec4\u4fe1\u606f \u6bcf\u4e2a\u6837\u672c\u5bf9\u5e94\u54ea\u4e2a\u5206\u7ec4<\/p>\n\n\n\n<p>caseGroup \u5b9e\u9a8c\u7ec4 \u54ea\u4e2a\u5206\u7ec4\u662f\u5b9e\u9a8c\u7ec4<\/p>\n\n\n\n<p>GOTERM2GENE\u3001GOTERM2NAME\u3001KEGGTERM2GENE\u3001KEGGTERM2NAME\u4e3a\u6ce8\u91ca\u6587\u4ef6\u4fe1\u606f<\/p>\n\n\n\n<p>MSigDB\uff08Molecular Signatures Database\uff09\u662f\u4e00\u4e2a\u5305\u542b\u6210\u5343\u4e0a\u4e07\u4e2a\u6ce8\u91ca\u57fa\u56e0\u96c6\u7684\u6570\u636e\u5e93\uff0c\u5206\u4e3a\u4eba\u7c7b\u548c\u9f20\u7c7b\u57fa\u56e0\u96c6\uff0c\u5e76\u4e14\u53ef\u4ee5\u901a\u8fc7\u5176\u5b98\u65b9\u7f51\u7ad9\u8fdb\u884c\u8bbf\u95ee\u548c\u4f7f\u7528\u3002\u6211\u4eec\u7684\u7269\u79cd\u4e3a\u975e\u6a21\u5f0f\u751f\u7269\uff0c\u8fd9\u6b65\u4f1a\u51fa\u73b0\u63d0\u9192\uff0c\u53ef\u4ee5\u5ffd\u7565\u3002<\/p>\n\n\n\n<p>object\u4e3a\u6784\u5efa\u7684\u5bf9\u8c61\uff0cdir\u8bbe\u7f6e\u7ed3\u679c\u6587\u4ef6\u7684\u4fdd\u5b58\u8def\u5f84\uff0c\u7ed3\u679c\u5305\u62ec\u6837\u672c\u95f4\u7684PCA\u56fe\u3001\u70ed\u56fe\u3001\u5206\u5e03\u56fe\u3001\u706b\u5c71\u56fe\u3001top\u5dee\u5f02\u57fa\u56e0\u7684\u8868\u8fbe\u70ed\u56fe\u3001\u591a\u79cd\u65b9\u6cd5\u7684Venn\u56fe\u7b49\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"188\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144789677_972D0915-1316-4a29-AA3D-F0F6AE21A4C7.png?resize=554%2C188\" alt=\"\" class=\"wp-image-61190\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144789677_972D0915-1316-4a29-AA3D-F0F6AE21A4C7.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144789677_972D0915-1316-4a29-AA3D-F0F6AE21A4C7.png?resize=300%2C102 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<h1 class=\"wp-block-heading\">l&nbsp;\u56db\uff1a\u7ed3\u679c\u89e3\u8bfb<strong><\/strong><\/h1>\n\n\n\n<p>\u6784\u5efa\u597d\u5bf9\u8c61\u540e\u4ec5\u9700\u4e00\u6b65\u5373\u53ef\u5b8c\u6210\u5168\u90e8\u7684\u4e0b\u6e38\u5206\u6790\uff01\u63a5\u4e0b\u6765\u5c0f\u679c\u5e26\u5927\u5bb6\u89e3\u8bfb\u4e00\u4e0b\u7ed3\u679c\u54e6\uff5e<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">1-run_check<strong><\/strong><\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">PCA\u56fe<\/h3>\n\n\n\n<p>\u6a2a\u7eb5\u5750\u6807\uff1a\u4e24\u4e2a\u7ef4\u5ea6<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"550\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144797795_EE973FCF-FD7E-42c8-9FE5-7C41480491CB.png?resize=554%2C550\" alt=\"\" class=\"wp-image-61191\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144797795_EE973FCF-FD7E-42c8-9FE5-7C41480491CB.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144797795_EE973FCF-FD7E-42c8-9FE5-7C41480491CB.png?resize=300%2C298 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144797795_EE973FCF-FD7E-42c8-9FE5-7C41480491CB.png?resize=150%2C150 150w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144797795_EE973FCF-FD7E-42c8-9FE5-7C41480491CB.png?resize=100%2C100 100w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\">boxplot\u56fe<\/h3>\n\n\n\n<p>\u6a2a\u5750\u6807\uff1a\u6837\u54c1\u540d<\/p>\n\n\n\n<p>\u7eb5\u5750\u6807\uff1alog2(cpm(count)+1)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"521\" height=\"277\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144806028_7F4644BD-D80B-4b03-91C0-ED532FA66D29.png?resize=521%2C277\" alt=\"\" class=\"wp-image-61192\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144806028_7F4644BD-D80B-4b03-91C0-ED532FA66D29.png?w=521 521w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144806028_7F4644BD-D80B-4b03-91C0-ED532FA66D29.png?resize=300%2C160 300w\" sizes=\"(max-width: 521px) 100vw, 521px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\">\u76f8\u5173\u6027\u56fe<strong><\/strong><\/h3>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"496\" height=\"498\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144816039_73B478CA-2050-45f0-8F83-257362B71C25.png?resize=496%2C498\" alt=\"\" class=\"wp-image-61193\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144816039_73B478CA-2050-45f0-8F83-257362B71C25.png?w=496 496w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144816039_73B478CA-2050-45f0-8F83-257362B71C25.png?resize=300%2C300 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144816039_73B478CA-2050-45f0-8F83-257362B71C25.png?resize=150%2C150 150w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144816039_73B478CA-2050-45f0-8F83-257362B71C25.png?resize=100%2C100 100w\" sizes=\"(max-width: 496px) 100vw, 496px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\">\u5206\u5e03\u56fe<\/h3>\n\n\n\n<p>boxplot\u56fe\u7684\u53e6\u4e00\u4e2a\u89c6\u89d2\uff0c\u8f6c\u6362\u4e86x\uff0cy\u8f74<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"200\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144824364_296EB0F5-E8EC-4527-B663-E0F31E3C7232.png?resize=554%2C200\" alt=\"\" class=\"wp-image-61194\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144824364_296EB0F5-E8EC-4527-B663-E0F31E3C7232.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144824364_296EB0F5-E8EC-4527-B663-E0F31E3C7232.png?resize=300%2C108 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\">\u70ed\u56fe<\/h3>\n\n\n\n<p>\u6a2a\u5750\u6807\uff1a\u6837\u672c<\/p>\n\n\n\n<p>\u7eb5\u5750\u6807\uff1a\u57fa\u56e0<\/p>\n\n\n\n<p>\u524d1000\u4e2a\u57fa\u56e0\u7ed8\u5236\u70ed\u56fe<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"510\" height=\"510\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144833545_4CB58D95-28D8-4825-B427-FCD36F5F20CE.png?resize=510%2C510\" alt=\"\" class=\"wp-image-61195\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144833545_4CB58D95-28D8-4825-B427-FCD36F5F20CE.png?w=510 510w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144833545_4CB58D95-28D8-4825-B427-FCD36F5F20CE.png?resize=300%2C300 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144833545_4CB58D95-28D8-4825-B427-FCD36F5F20CE.png?resize=150%2C150 150w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144833545_4CB58D95-28D8-4825-B427-FCD36F5F20CE.png?resize=100%2C100 100w\" sizes=\"(max-width: 510px) 100vw, 510px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">2-runDEG<strong><\/strong><\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">\u70ed\u56fe<\/h3>\n\n\n\n<p>\u4e09\u79cd\u65b9\u6848\u524d500\u4e2a\u57fa\u56e0\u7ed8\u5236\u7684\u70ed\u56fe<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"185\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144843965_8DBB1E19-750F-4126-86FC-F515B8F6264A.png?resize=554%2C185\" alt=\"\" class=\"wp-image-61196\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144843965_8DBB1E19-750F-4126-86FC-F515B8F6264A.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1729144843965_8DBB1E19-750F-4126-86FC-F515B8F6264A.png?resize=300%2C100 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\">\u706b\u5c71\u56fe<\/h3>\n\n\n\n<p>\u6a2a\u5750\u6807\uff1alog2\uff08Fold Change\uff09<\/p>\n\n\n\n<p>\u7eb5\u5750\u6807\uff1a-log10\uff08p-value\uff09<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" 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