{"id":61028,"date":"2024-10-11T14:30:10","date_gmt":"2024-10-11T06:30:10","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61028"},"modified":"2024-10-11T14:30:10","modified_gmt":"2024-10-11T06:30:10","slug":"%e5%a4%9a%e7%a7%8d%e5%8d%95%e7%bb%86%e8%83%9e%e5%af%8c%e9%9b%86%e8%af%84%e5%88%86%e7%ae%97%e6%b3%95%e6%89%93%e5%8c%85%e5%88%b0r%e5%8c%85irgsea%ef%bc%81%e6%89%b9%e9%87%8f%e8%af%84%e5%88%86%e6%96%b9","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61028","title":{"rendered":"\u591a\u79cd\u5355\u7ec6\u80de\u5bcc\u96c6\u8bc4\u5206\u7b97\u6cd5\u6253\u5305\u5230R\u5305irGSEA\uff01\u6279\u91cf\u8bc4\u5206\u65b9\u6cd5\u51cf\u5c11\u5f15\u5165\u504f\u5dee\uff01"},"content":{"rendered":"\n<p><strong>\u524d\u8a00<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u5c0f\u4f19\u4f34\u4eec\u90fd\u8d8b\u5411\u4e8e\u4f7f\u7528\u672a\u6821\u6b63\u6279\u6b21\u6548\u5e94\u540e\u7684\u6570\u636e\u8fdb\u884c\u5dee\u5f02\u57fa\u56e0\u5206\u6790\uff0c\u4f46\u662f\u5728\u5bcc\u96c6\u5206\u6790\u7684\u8fc7\u7a0b\u4e2d\uff0c\u4f7f\u7528\u6821\u6b63\u540e\u7684\u6570\u636e\u8fd8\u662f\u672a\u6821\u6b63\u6279\u6b21\u6548\u5e94\u540e\u7684\u6570\u636e\u5462\uff1f\u6821\u6b63\u6279\u6b21\u6548\u5e94\u540e\u7684\u6570\u636e\u4f1a\u4e0d\u4f1a\u63a9\u76d6\u90e8\u5206\u771f\u5b9e\u7684\u751f\u7269\u5b66\u5dee\u5f02\uff1f\u6837\u672c\u4e4b\u95f4\u7684\u6279\u6b21\u6548\u5e94\u662f\u5426\u4f1a\u5f71\u54cd\u57fa\u56e0\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u4ecd\u7136\u662f\u4e00\u4e2a\u4e89\u8bba\u3002\u4eca\u5929\u5927\u6d77\u54e5\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u7684\u65b9\u6cd5\u91cd\u65b0\u5ba1\u89c6\u73b0\u6709\u7684\u3001\u4e3b\u6d41\u7684\u57fa\u56e0\u96c6\u5bcc\u96c6\u65b9\u6cd5\uff0c\u627e\u5230\u53d7\u6279\u6b21\u6548\u5e94\u5f71\u54cd\u8f83\u5c0f\u7684\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u3002\u50cf\u5c0f\u4f19\u4f34\u4eec\u719f\u6089\u7684AUCell\u3001UCell\u3001singscore\u3001ssGSEA\u3001JASMINE \u548c Viper\u88ab\u6253\u5305\u5230R\u5305irGSEA\u3002\u901a\u8fc7\u91c7\u7528\u9c81\u68d2\u79e9\u805a\u5408\u7b97\u6cd5\uff0c<a>irGSEA<\/a>\u5408\u5e76\u4e86\u6240\u6709\u516d\u79cd\u65b9\u6cd5\u7684\u7ed3\u679c\uff0c\u4ee5\u786e\u5b9a\u76ee\u6807\u57fa\u56e0\u96c6\u5728\u4e0d\u540c\u8bc4\u5206\u65b9\u6cd5\u4e2d\u7684\u7edf\u8ba1\u5b66\u610f\u4e49\u3002irGSEA\u91c7\u7528\u57fa\u4e8e\u6279\u91cf\u7684\u8bc4\u5206\u65b9\u6cd5\u53ef\u4ee5\u51cf\u5c11\u4ec5\u91c7\u7528\u5355\u7ec6\u80de\u8bc4\u5206\u65b9\u6cd5\u5f15\u5165\u7684\u504f\u5dee\u3002\u8be5\u6846\u67b6\u7ed3\u5408\u4e86RRA\u65b9\u6cd5\uff0c\u4ee5\u5728\u5404\u79cd\u8bc4\u5206\u65b9\u6cd5\u4e2d\u8bc6\u522b\u663e\u7740\u5bcc\u96c6\u7684\u57fa\u56e0\u96c6\u3002<\/p>\n\n\n\n<p><strong>irGSEA\u8981\u70b9\uff1a<\/strong><strong><\/strong><\/p>\n\n\n\n<ul>\n<li>irGSEA\u901a\u8fc7\u91c7\u7528\u9c81\u68d2\u7684\u79e9\u805a\u5408\u7b97\u6cd5\u6765\u5408\u5e76\u6240\u6709\u516d\u79cd\u57fa\u4e8e\u79e9\u7684\u65b9\u6cd5\u7684\u7ed3\u679c\uff0c\u4ee5\u786e\u5b9a\u76ee\u6807\u57fa\u56e0\u96c6\u5728\u4e0d\u540c\u8bc4\u5206\u65b9\u6cd5\u4e2d\u7684\u7edf\u8ba1\u5b66\u610f\u4e49\u3002<\/li>\n\n\n\n<li>irGSEA\u652f\u630119\u79cd\u57fa\u56e0\u96c6\u8bc4\u5206\u65b9\u6cd5\uff0c\u5e76\u96c6\u6210\u4e86\u591a\u79cd\u7528\u6237\u53cb\u597d\u7684\u53ef\u89c6\u5316\u5de5\u5177\u6765\u663e\u793a\u7ed3\u679c\u3002<\/li>\n\n\n\n<li>irGSEA\u6709\u52a9\u4e8e\u8bc4\u4f30\u7ec6\u80de\u7c07\u5185\u53ef\u80fd\u5177\u6709\u91cd\u8981\u610f\u4e49\u7684\u751f\u7269\u8fc7\u7a0b\uff0c\u5f3a\u8c03\u5176\u5728\u63a2\u7d22\u7ec6\u80de\u529f\u80fd\u65b9\u9762\u7684\u5b9e\u7528\u6027\uff0c\u800c\u4e0d\u662f\u5728\u7ec6\u80de\u7c7b\u578b\u9274\u5b9a\u65b9\u9762\u8868\u73b0\u51fa\u8272\u3002<\/li>\n<\/ul>\n\n\n\n<p>\u5927\u6d77\u54e5\u5c31\u662f\u8fd9\u4e48\u7684\u5ba0\u7c89\uff0c\u6709\u4ec0\u4e48\u751f\u4fe1\u5206\u6790\u4e0a\u7684\u95ee\u9898\u5927\u5bb6\u5c3d\u7ba1\u54a8\u8be2\u5927\u6d77\u54e5\uff01\u6ca1\u6709\u65f6\u95f4\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\u4eec\u4e5f\u4e0d\u8981\u7740\u6025\u54e6\uff01\u6709\u9700\u8981\u751f\u4fe1\u5206\u6790\u7684\u5c0f\u4f19\u4f34\u4eec\u4e5f\u53ef\u4ee5\u627e\u5927\u6d77\u54e5\u54e6\uff01\u7ec3\u4e86\u5341\u5e74\u751f\u4fe1\u5206\u6790\u7684\u5927\u6d77\u54e5\u5bf9\u4e8e\u751f\u4fe1\u5206\u6790\u77e5\u8bc6\u5df2\u7ecf\u5982\u9c7c\u5f97\u6c34\u4ece\u5206\u6790\u5230\u53ef\u89c6\u5316\u76f4\u5230\u4f60\u6ee1\u610f\u4e3a\u6b62\uff01<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"520\" height=\"451\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627712651_C525B5C1-6AC1-43e1-B426-F5E0CB616977.png?resize=520%2C451\" alt=\"\" class=\"wp-image-61029\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627712651_C525B5C1-6AC1-43e1-B426-F5E0CB616977.png?w=520 520w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627712651_C525B5C1-6AC1-43e1-B426-F5E0CB616977.png?resize=300%2C260 300w\" sizes=\"(max-width: 520px) 100vw, 520px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u751f\u4fe1\u6570\u636e\u5904\u7406\u8d77\u6765\u5360\u7528\u5185\u5b58\u5b9e\u5728\u592a\u5927\u4e86\uff0c\u653e\u8fc7\u81ea\u5df1\u7684\u7535\u8111\u5427\uff01\u5927\u6d77\u54e5\u5728\u8fd9\u91cc\u7ed9\u5927\u5bb6\u9001\u4e0a\u798f\u5229\u4e86\uff0c\u6709\u9700\u8981\u670d\u52a1\u5668\u7684\u5c0f\u4f19\u4f34\u4eec\uff0c\u6b22\u8fce\u5927\u5bb6\u8054\u7cfb\u5927\u6d77\u54e5\uff0c\u4fdd\u8bc1\u670d\u52a1\u5668\u7684\u6027\u4ef7\u6bd4\u6700\u9ad8\u54e6\uff01<\/p>\n\n\n\n<p><strong>\u4ee3\u7801\u6559\u7a0b<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>1.\u5b89\u88c5\u524d\u7684\u51c6\u5907<\/strong><strong><\/strong><\/p>\n\n\n\n<p>R\u5305irGSEA\u6dd8\u6c70\u4e86\u6240\u6709\u9700\u8981\u8003\u8651\u6837\u672c\u7ec4\u6210\u7684\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\uff0c\u9009\u53d6\u4e86\u57fa\u4e8e\u5355\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u6392\u540d\u7684\u57fa\u56e0\u96c6\u5206\u6790\u65b9\u6cd5\uff1aAUCell\u3001UCell\u548csingscore\u3002\u540c\u65f6\uff0c\u4e5f\u90e8\u5206\u6539\u8fdb\u4e86ssGSEA\uff0c\u53d6\u6d88\u6700\u540e\u7684\u6807\u51c6\u5316\u6b65\u9aa4\uff0c\u4f7f\u4e4b\u66f4\u8d34\u8fd1\u4e8e\u5355\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u3002<\/p>\n\n\n\n<p>\u5728\u5b89\u88c5irGSEA \u9700\u8981\u67e5\u770b\u81ea\u5df1\u662f\u5426\u5b89\u88c5\u4e86\u4ee5\u4e0b\u8fd9\u4e9b\u5305\u3002<\/p>\n\n\n\n<p># \u4ece CRAN\u5b89\u88c5R\u5305<\/p>\n\n\n\n<p>cran.packages &lt;- c(&#8220;msigdbr&#8221;, &#8220;dplyr&#8221;, &#8220;purrr&#8221;, &#8220;stringr&#8221;,&#8221;magrittr&#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;&#8220;RobustRankAggreg&#8221;, &#8220;tibble&#8221;, &#8220;reshape2&#8221;, &#8220;ggsci&#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;&#8220;tidyr&#8221;, &#8220;aplot&#8221;, &#8220;ggfun&#8221;, &#8220;ggplotify&#8221;, &#8220;ggridges&#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;&#8220;gghalves&#8221;, &#8220;Seurat&#8221;, &#8220;SeuratObject&#8221;, &#8220;methods&#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;&#8220;devtools&#8221;, &#8220;BiocManager&#8221;,&#8221;data.table&#8221;,&#8221;doParallel&#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;&#8220;doRNG&#8221;)<\/p>\n\n\n\n<p>if (!requireNamespace(cran.packages, quietly = TRUE)) {<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;install.packages(cran.packages, ask = F, update = F)<\/p>\n\n\n\n<p>}<\/p>\n\n\n\n<p>#\u4eceBioconductor\u5b89\u88c5R\u5305<\/p>\n\n\n\n<p>bioconductor.packages &lt;- c(&#8220;GSEABase&#8221;, &#8220;AUCell&#8221;, &#8220;SummarizedExperiment&#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;&#8220;singscore&#8221;, &#8220;GSVA&#8221;, &#8220;ComplexHeatmap&#8221;, &#8220;ggtree&#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;&#8220;Nebulosa&#8221;)<\/p>\n\n\n\n<p>if (!requireNamespace(bioconductor.packages, quietly = TRUE)) {<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;BiocManager::install(bioconductor.packages, ask = F, update = F)<\/p>\n\n\n\n<p>}<\/p>\n\n\n\n<p>#\u4eceGithub\u5b89\u88c5R\u5305<\/p>\n\n\n\n<p>if (!requireNamespace(&#8220;UCell&#8221;, quietly = TRUE)) {<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;devtools::install_github(&#8220;carmonalab\/UCell&#8221;)<\/p>\n\n\n\n<p>}<\/p>\n\n\n\n<p>if (!requireNamespace(&#8220;irGSEA&#8221;, quietly = TRUE)) {<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;devtools::install_github(&#8220;chuiqin\/irGSEA&#8221;)<\/p>\n\n\n\n<p>}<\/p>\n\n\n\n<p><strong>2.\u52a0\u8f7d\u793a\u4f8b\u6570\u636e<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6211\u4eec\u5141\u8bb8\u76f4\u63a5\u8f93\u5165\u5355\u7ec6\u80de\u8868\u8fbe\u77e9\u9635\u6216\u8005Seurat\u5bf9\u8c61\u3002\u6211\u4eec\u5185\u7f6e\u4e86Seurat\u5305\uff0c\u53ef\u4ee5\u5c06\u591a\u79cd\u57fa\u56e0\u96c6\u7684\u5bcc\u96c6\u5206\u6570\u77e9\u9635\u76f4\u63a5\u4fdd\u5b58\u5230Seurat\u5bf9\u8c61\u4e2d\u3002\u540c\u65f6\uff0c\u6211\u4eec\u4e5f\u652f\u6301\u8fc7\u6ee4\u5355\u7ec6\u80de\u8868\u8fbe\u77e9\u9635\u4e2d\u6240\u6709\u7ec6\u80de\u8868\u8fbe\u91cf\u4e3a0\u7684\u57fa\u56e0\u3002\u5f53\u7136\uff0c\u7528\u6237\u4e5f\u53ef\u4ee5\u81ea\u5b9a\u4e49\u81ea\u5df1\u7684\u8fc7\u6ee4\u6807\u51c6\u3002\u5408\u9002\u7684\u8fc7\u6ee4\u6307\u6807\u53ef\u4ee5\u6539\u5584\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\u3002<\/p>\n\n\n\n<p>\u6211\u4eec\u901a\u8fc7SeuratData\u5305\u52a0\u8f7d\u793a\u4f8b\u6570\u636e\u96c6\uff08\u6ce8\u91ca\u597d\u7684PBMC\u6570\u636e\u96c6\uff09<\/p>\n\n\n\n<p># devtools::install_github(&#8216;satijalab\/seurat-data&#8217;)<\/p>\n\n\n\n<p>library(SeuratData)<\/p>\n\n\n\n<p># view all available datasets<\/p>\n\n\n\n<p>View(AvailableData())<\/p>\n\n\n\n<p># download 3k PBMCs from 10X Genomics<\/p>\n\n\n\n<p># \u793a\u4f8b\u6570\u636e\u6709\u70b9\u5927\uff0c\u5efa\u8bae\u5728\u7f51\u901f\u597d\u7684\u65f6\u5019\u4e0b\u8f7d\uff0c\u5982\u679c\u5931\u8d25\u4e86\uff0c\u8bf7\u91cd\u542fR\u540e\u591a\u5c1d\u8bd5\u51e0\u904d<\/p>\n\n\n\n<p>InstallData(&#8220;pbmc3k&#8221;)<\/p>\n\n\n\n<p># the details of pbmc3k.final<\/p>\n\n\n\n<p>?pbmc3k.final<\/p>\n\n\n\n<p>library(Seurat)<\/p>\n\n\n\n<p>library(SeuratData)<\/p>\n\n\n\n<p>#\u52a0\u8f7d\u6570\u636e<\/p>\n\n\n\n<p>data(&#8220;pbmc3k.final&#8221;)<\/p>\n\n\n\n<p>pbmc3k.final &lt;- UpdateSeuratObject(pbmc3k.final)<\/p>\n\n\n\n<p>#\u7ed8\u56fe<\/p>\n\n\n\n<p>DimPlot(pbmc3k.final, reduction = &#8220;umap&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;group.by = &#8220;seurat_annotations&#8221;,label = T) + NoLegend()<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"509\" height=\"307\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627759503_B3979712-D0DF-4769-9687-17FA9AB127B4.png?resize=509%2C307\" alt=\"\" class=\"wp-image-61030\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627759503_B3979712-D0DF-4769-9687-17FA9AB127B4.png?w=509 509w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627759503_B3979712-D0DF-4769-9687-17FA9AB127B4.png?resize=300%2C181 300w\" sizes=\"(max-width: 509px) 100vw, 509px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u987a\u624b\u8bbe\u7f6e\u4e00\u4e0b\u6570\u636e\u96c6\u7684ident<\/p>\n\n\n\n<p># set cluster to idents<\/p>\n\n\n\n<p>Idents(pbmc3k.final) &lt;- pbmc3k.final$seurat_annotations<\/p>\n\n\n\n<p><strong>3.\u52a0\u8f7dR\u5305<\/strong><strong><\/strong><\/p>\n\n\n\n<p>library(UCell)<\/p>\n\n\n\n<p>library(irGSEA)<\/p>\n\n\n\n<p><strong>4.\u8ba1\u7b97\u5bcc\u96c6\u5206\u6570<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u5f53\u4f60\u7684ncore\u8bbe\u7f6e\u5927\u4e8e1\u7684\u65f6\u5019\uff0c\u53d1\u751f\u4e0b\u9762\u7684\u9519\u8bef\uff1aError (Valid \u2018mctype\u2019: \u2018snow\u2019 or \u2018doMC\u2019)\uff0c\u4f60\u5e94\u8be5\u68c0\u67e5\u4e00\u4e0b\u4f60\u7684AUCell \u7248\u672c\uff0c\u786e\u4fdd\u7248\u672c\u5927\u4e8e\u7b49\u4e8e1.14 \u3002\u5982\u679c\u4f60\u6bd4\u8f83\u61d2\uff0c\u90a3\u4f60\u76f4\u63a5\u628ancore\u8bbe\u7f6e\u4e3a1\u4e5f\u662f\u53ef\u4ee5\u7684\uff0c\u53ea\u662f\u8fd0\u884c\u901f\u5ea6\u4f1a\u7a0d\u5fae\u6162\u4e00\u70b9\u3002<\/p>\n\n\n\n<p>pbmc3k.final &lt;- irGSEA.score(object = pbmc3k.final, assay = &#8220;RNA&#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;slot = &#8220;data&#8221;, seeds = 123, ncores = 1,<\/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;min.cells = 3, min.feature = 0,<\/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;custom = F, geneset = NULL, msigdb = T,<\/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;species = &#8220;Homo sapiens&#8221;, category = &#8220;H&#8221;, &nbsp;<\/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;subcategory = NULL, geneid = &#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;method = c(&#8220;AUCell&#8221;, &#8220;UCell&#8221;, &#8220;singscore&#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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&#8220;ssgsea&#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;aucell.MaxRank = NULL, ucell.MaxRank = NULL,<\/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;kcdf = &#8216;Gaussian&#8217;)<\/p>\n\n\n\n<p># \u8fd4\u56de\u4e00\u4e2aSeurat\u5bf9\u8c61\uff0c\u5bcc\u96c6\u5206\u6570\u77e9\u9635\u5b58\u653e\u5728RNA\u5916\u7684assay\u4e2d<\/p>\n\n\n\n<p>Seurat::Assays(pbmc3k.final)<\/p>\n\n\n\n<p><strong>5.\u6574\u5408\u5dee\u5f02\u57fa\u56e0\u96c6<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u4e3a\u4e86\u8bc4\u4f30\u57fa\u56e0\u96c6\u5728\u67d0\u4e2a\u7ec6\u80de\u4e9a\u7fa4\u4e2d\u662f\u5426\u5bcc\u96c6\uff0c\u901a\u8fc7\u591a\u79cd\u57fa\u56e0\u96c6\u5bcc\u96c6\u65b9\u6cd5\u5206\u522b\u5bf9\u5355\u4e2a\u7ec6\u80de\u8fdb\u884c\u6253\u5206\uff0c\u5e76\u751f\u6210\u591a\u4e2a\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6570\u77e9\u9635\u3002\u63a5\u7740\uff0c\u901a\u8fc7wilcox\u68c0\u9a8c\u8ba1\u7b97\u5404\u4e2a\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6570\u77e9\u9635\u4e2d\u6bcf\u4e2a\u7ec6\u80de\u4e9a\u7fa4\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\u96c6\u3002<\/p>\n\n\n\n<p>\u5355\u4e00\u7684\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u4e0d\u4ec5\u53ea\u80fd\u53cd\u6620\u6709\u9650\u7684\u4fe1\u606f\uff0c\u800c\u4e14\u4e5f\u5bb9\u6613\u5e26\u6765\u8bef\u5dee\u3002\u671f\u5f85\u4ece\u591a\u4e2a\u89d2\u5ea6\u89e3\u91ca\u590d\u6742\u7684\u751f\u7269\u5b66\u95ee\u9898\uff0c\u5e76\u627e\u5230\u751f\u7269\u5b66\u95ee\u9898\u4e2d\u7684\u5171\u6027\u90e8\u5206\u3002\u7b80\u5355\u5730\u4e3a\u591a\u79cd\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u7684\u7ed3\u679c\u53d6\u5171\u540c\u4ea4\u96c6\uff0c\u4e0d\u4ec5\u5bb9\u6613\u5f97\u5230\u5c11\u800c\u4fdd\u5b88\u7684\u7ed3\u679c\uff0c\u800c\u4e14\u5ffd\u7565\u4e86\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u4e2d\u5f88\u591a\u7684\u5176\u4ed6\u4fe1\u606f\uff0c\u4f8b\u5982\u4e0d\u540c\u57fa\u56e0\u96c6\u7684\u76f8\u5bf9\u5bcc\u96c6\u7a0b\u5ea6\u4fe1\u606f\u3002<\/p>\n\n\n\n<p>\u5355\u7eaf\u5730\u53d6\u5171\u540c\u4ea4\u96c6\u65e0\u6cd5\u4f53\u73b0\u57fa\u56e0\u96c6\u7684\u76f8\u5bf9\u5bcc\u96c6\u7a0b\u5ea6\uff0c\u5e0c\u671b\u76ee\u6807\u57fa\u56e0\u96c6\u5728\u5927\u90e8\u5206\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u4e2d\u90fd\u662f\u5bcc\u96c6\u4e14\u5bcc\u96c6\u7a0b\u5ea6\u6ca1\u6709\u660e\u663e\u5dee\u5f02\u3002\u56e0\u6b64\uff0c\u901a\u8fc7RobustRankAggreg\u5305\u4e2d\u7684\u79e9\u805a\u5408\u7b97\u6cd5(robust rank aggregation, RRA)\u5bf9\u5dee\u5f02\u5206\u6790\u7684\u7ed3\u679c\u8fdb\u884c\u7efc\u5408\u8bc4\u4f30\uff0c\u7b5b\u9009\u51fa\u5728\u5927\u90e8\u5206\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u4e2d\u90fd\u663e\u8457\u5bcc\u96c6\u7684\u57fa\u56e0\u96c6\u3002<\/p>\n\n\n\n<p>result.dge &lt;- irGSEA.integrate(object = pbmc3k.final,<\/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;&nbsp;group.by = &#8220;seurat_annotations&#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;&nbsp;metadata = NULL, col.name = NULL,<\/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;&nbsp;method = c(&#8220;AUCell&#8221;,&#8221;UCell&#8221;,&#8221;singscore&#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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&#8220;ssgsea&#8221;))<\/p>\n\n\n\n<p>class(result.dge)<\/p>\n\n\n\n<p><strong>6.\u53ef\u89c6\u5316\u5c55\u793a<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6211\u4eec\u5185\u7f6e\u4e86\u591a\u79cd\u53ef\u89c6\u5316\u7684\u51fd\u6570\uff0c\u4e0d\u4ec5\u5141\u8bb8\u7528\u6237\u901a\u8fc7\u70ed\u56fe\u3001\u6c14\u6ce1\u56fe\u3001\u67f1\u72b6\u56fe\u548cupset\u56fe\u5c55\u793a\u5b83\u4eec\u7efc\u5408\u7ed3\u679c\uff0c\u800c\u4e14\u5141\u8bb8\u7528\u6237\u901a\u8fc7\u5bc6\u5ea6\u6563\u70b9\u56fe\u3001\u534a\u5c0f\u63d0\u7434\u56fe\u3001\u5c71\u5ce6\u56fe\u548c\u5bc6\u5ea6\u70ed\u56fe\u5c55\u793a\u76ee\u6807\u57fa\u56e0\u96c6\u5728\u5177\u4f53\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u4e2d\u7684\u8868\u8fbe\u6c34\u5e73\u548c\u6570\u636e\u5206\u5e03\u3002\u5176\u4e2d\uff0c\u70ed\u56fe\u3001upset\u56fe\u3001\u5bc6\u5ea6\u70ed\u56fe\u4e3b\u8981\u7531ComplexHeatmap\u5305\u751f\u6210\uff1b\u6c14\u6ce1\u56fe\u548c\u67f1\u72b6\u56fe\u4e3b\u8981\u7531ggplot2\u5305\u3001ggtree\u5305\u3001aplot\u5305\u751f\u6210\uff1b\u5bc6\u5ea6\u6563\u70b9\u56fe\u4e3b\u8981\u7531Seurat\u5305\u548cNebulosa\u5305\u751f\u6210\uff0c\u534a\u5c0f\u63d0\u7434\u56fe\u4e3b\u8981\u7531Seurat\u5305\u548cgghalves\u5305\u751f\u6210\uff1b\u5c71\u5ce6\u56fe\u4e3b\u8981\u7531Seurat\u5305\u548cggridges\u5305\u751f\u6210\u3002\u6700\u540e\uff0c\u4e3a\u4e86\u65b9\u4fbf\u7528\u6237\u5c06\u53ef\u89c6\u5316\u7ed3\u679c\u4e0e\u5176\u4ed6\u7684ggplot2\u5bf9\u8c61\u8fdb\u884c\u62fc\u56fe\u64cd\u4f5c\uff0c\u6211\u4eec\u4e5f\u901a\u8fc7ggplotify\u5305\u628a\u8f93\u51fa\u7ed3\u679c\u8f6c\u6362\u4e3aggplot2\u5bf9\u8c61\u3002<\/p>\n\n\n\n<p>\u4f5c\u8005\uff1a\u8303\u5782\u94a6_92be<\/p>\n\n\n\n<p>\u94fe\u63a5\uff1ahttps:\/\/www.jianshu.com\/p\/463dd6e2986f<\/p>\n\n\n\n<p>\u6765\u6e90\uff1a\u7b80\u4e66<\/p>\n\n\n\n<p>\u8457\u4f5c\u6743\u5f52\u4f5c\u8005\u6240\u6709\u3002\u5546\u4e1a\u8f6c\u8f7d\u8bf7\u8054\u7cfb\u4f5c\u8005\u83b7\u5f97\u6388\u6743\uff0c\u975e\u5546\u4e1a\u8f6c\u8f7d\u8bf7\u6ce8\u660e\u51fa\u5904\u3002<\/p>\n\n\n\n<p>1\uff09. \u5168\u5c40\u5c55\u793a<\/p>\n\n\n\n<p>\u2460.\u70ed\u56fe<\/p>\n\n\n\n<p>\u70ed\u56fe\u5c55\u793a\u4e86\u7efc\u5408\u8bc4\u4ef7\u4e2d\u5177\u4f53\u57fa\u56e0\u96c6\u5728\u6bcf\u4e2a\u7ec6\u80de\u4e9a\u7fa4\u662f\u5426\u5177\u6709\u7edf\u8ba1\u5b66\u610f\u4e49\u5dee\u5f02\uff1b<\/p>\n\n\n\n<p>\u5176\u4e2d\uff0c\u6d45\u84dd\u8272\u7684\u683c\u5b50\u65e0\u7edf\u8ba1\u5b66\u5dee\u5f02\uff0c\u7ea2\u8272\u7684\u683c\u5b50\u5177\u6709\u7edf\u8ba1\u5b66\u5dee\u5f02\u3002\u683c\u5b50\u4e2d\u7684\u661f\u53f7\u8d8a\u591a\uff0c\u683c\u5b50\u7684P\u503c\u8d8a\u5c0f\uff1b<\/p>\n\n\n\n<p>\u5de6\u8fb9\u7684\u805a\u7c7b\u6811\u4ee3\u8868\u4e0d\u540c\u57fa\u56e0\u96c6\u5728\u4e0d\u540c\u7ec6\u80de\u4e9a\u7fa4\u4e2d\u8868\u8fbe\u6a21\u5f0f\u7684\u76f8\u4f3c\u6027\uff1b<\/p>\n\n\n\n<p>\u4e0a\u65b9\u7684\u6761\u5f62\u56fe\u5206\u522b\u4ee3\u8868\u4e0d\u540c\u7684\u7ec6\u80de\u4e9a\u7fa4\uff0c\u4ee5\u53ca\u5dee\u5f02\u57fa\u56e0\u96c6\u5728\u7ec6\u80de\u4e9a\u7fa4\u4e2d\u662f\u5448\u73b0\u4e0a\u8c03\u8fd8\u662f\u4e0b\u8c03\u8d8b\u52bf\uff1b<\/p>\n\n\n\n<p>\u4f60\u8fd8\u53ef\u4ee5\u628amethod\u4ece&#8217;RRA&#8221;\u6362\u6210\u201cssgsea\u201d\uff0c\u5c55\u793a\u7279\u5b9a\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u4e2d\u5dee\u5f02\u4e0a\u8c03\u6216\u5dee\u5f02\u4e0b\u8c03\u7684\u57fa\u56e0\u96c6\uff1b<\/p>\n\n\n\n<p>irGSEA.heatmap.plot &lt;- irGSEA.heatmap(object = result.dge,<\/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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;method = &#8220;RRA&#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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;top = 50,<\/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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;show.geneset = NULL)<\/p>\n\n\n\n<p>irGSEA.heatmap.plot<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"553\" height=\"332\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627796504_EABC94C7-08DB-44ae-A95F-64A4126FEF70.png?resize=553%2C332\" alt=\"\" class=\"wp-image-61031\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627796504_EABC94C7-08DB-44ae-A95F-64A4126FEF70.png?w=553 553w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627796504_EABC94C7-08DB-44ae-A95F-64A4126FEF70.png?resize=300%2C180 300w\" sizes=\"(max-width: 553px) 100vw, 553px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u2461.\u6c14\u6ce1\u56fe<\/p>\n\n\n\n<p>\u6c14\u6ce1\u56fe\u5c55\u793a\u4e86\u7efc\u5408\u8bc4\u4ef7\u4e2d\u5177\u4f53\u57fa\u56e0\u96c6\u5728\u6bcf\u4e2a\u7ec6\u80de\u4e9a\u7fa4\u662f\u5426\u5177\u6709\u7edf\u8ba1\u5b66\u610f\u4e49\u5dee\u5f02\uff1b<\/p>\n\n\n\n<p>\u5176\u4e2d\uff0c\u6d45\u84dd\u8272\u7684\u70b9\u65e0\u7edf\u8ba1\u5b66\u5dee\u5f02\uff0c\u7ea2\u8272\u7684\u70b9\u5177\u6709\u7edf\u8ba1\u5b66\u5dee\u5f02\u3002\u70b9\u8d8a\u5927\uff0cP\u503c\u8d8a\u5c0f\uff1b<\/p>\n\n\n\n<p>\u5de6\u8fb9\u7684\u805a\u7c7b\u6811\u4ee3\u8868\u4e0d\u540c\u57fa\u56e0\u96c6\u5728\u4e0d\u540c\u7ec6\u80de\u4e9a\u7fa4\u4e2d\u8868\u8fbe\u6a21\u5f0f\u7684\u76f8\u4f3c\u6027\uff1b<\/p>\n\n\n\n<p>\u4e0a\u65b9\u7684\u6761\u5f62\u56fe\u5206\u522b\u4ee3\u8868\u4e0d\u540c\u7684\u7ec6\u80de\u4e9a\u7fa4\uff0c\u4ee5\u53ca\u5dee\u5f02\u57fa\u56e0\u96c6\u5728\u76ee\u6807\u7ec6\u80de\u4e9a\u7fa4\u4e2d\u662f\u5448\u73b0\u4e0a\u8c03\u8fd8\u662f\u4e0b\u8c03\u8d8b\u52bf\uff1b<\/p>\n\n\n\n<p>\u4f60\u8fd8\u53ef\u4ee5\u628amethod\u4ece&#8217;RRA&#8221;\u6362\u6210\u201cssgsea\u201d\uff0c\u5c55\u793a\u7279\u5b9a\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u4e2d\u5dee\u5f02\u4e0a\u8c03\u6216\u5dee\u5f02\u4e0b\u8c03\u7684\u57fa\u56e0\u96c6\uff1b<\/p>\n\n\n\n<p>\u5982\u679c\u8fd0\u884c\u4e2d\u63d0\u793a\u201c error (argument \u201ccaller_env\u201d is missing, with no default)\u201d\uff0c\u8bf7\u5378\u8f7d\u4e86ggtree\u5305\uff0c\u5e76\u91cd\u65b0\u5b89\u88c5remotes::install_github(\u201dYuLab-SMU\/ggtree\u201c)<\/p>\n\n\n\n<p>irGSEA.bubble.plot &lt;- irGSEA.bubble(object = result.dge,<\/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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;method = &#8220;RRA&#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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;top = 50)<\/p>\n\n\n\n<p>irGSEA.bubble.plot<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"541\" height=\"268\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627827342_C7DF8775-4A54-45a1-B407-25185B7054CD.png?resize=541%2C268\" alt=\"\" class=\"wp-image-61032\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627827342_C7DF8775-4A54-45a1-B407-25185B7054CD.png?w=541 541w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627827342_C7DF8775-4A54-45a1-B407-25185B7054CD.png?resize=300%2C149 300w\" sizes=\"(max-width: 541px) 100vw, 541px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u2462.upset plot<\/p>\n\n\n\n<p>upset\u56fe\u5c55\u793a\u4e86\u7efc\u5408\u8bc4\u4f30\u4e2d\u6bcf\u4e2a\u7ec6\u80de\u4e9a\u7fa4\u5177\u6709\u7edf\u8ba1\u5b66\u610f\u4e49\u5dee\u5f02\u7684\u57fa\u56e0\u96c6\u7684\u6570\u76ee\uff0c\u4ee5\u53ca\u4e0d\u540c\u7ec6\u80de\u4e9a\u7fa4\u4e4b\u95f4\u5177\u6709\u4ea4\u96c6\u7684\u5dee\u5f02\u57fa\u56e0\u96c6\u6570\u76ee\uff1b<\/p>\n\n\n\n<p>\u5de6\u8fb9\u4e0d\u540c\u989c\u8272\u7684\u6761\u5f62\u56fe\u4ee3\u8868\u4e0d\u540c\u7684\u7ec6\u80de\u4e9a\u7fa4\uff1b<\/p>\n\n\n\n<p>\u4e0a\u65b9\u7684\u6761\u5f62\u56fe\u4ee3\u8868\u5177\u6709\u4ea4\u96c6\u7684\u5dee\u5f02\u57fa\u56e0\u96c6\u7684\u6570\u76ee\uff1b<\/p>\n\n\n\n<p>\u4e2d\u95f4\u7684\u6c14\u6ce1\u56fe\u5355\u4e2a\u70b9\u4ee3\u8868\u5355\u4e2a\u7ec6\u80de\u4e9a\u7fa4\uff0c\u591a\u4e2a\u70b9\u8fde\u7ebf\u4ee3\u8868\u591a\u4e2a\u7ec6\u80de\u4e9a\u7fa4\u53d6\u4ea4\u96c6.\uff1b<\/p>\n\n\n\n<p>\u5982\u679c\u8fd0\u884c\u4ee3\u7801\u53d1\u751f\u4ee5\u4e0bwarning\u201cthe condition has length &gt; 1 and<\/p>\n\n\n\n<p>only the first element will be used\u201d\u3002\u8fd9\u4e2a\u8b66\u544a\u53ef\u5ffd\u7565\u3002<\/p>\n\n\n\n<p>irGSEA.upset.plot &lt;- irGSEA.upset(object = result.dge,<\/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;&nbsp;&nbsp;&nbsp;&nbsp;method = &#8220;RRA&#8221;)<\/p>\n\n\n\n<p>irGSEA.upset.plot<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"549\" height=\"297\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627867275_F7ADD81B-4127-4c7d-AC8B-1B2AC737F78D.png?resize=549%2C297\" alt=\"\" class=\"wp-image-61033\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627867275_F7ADD81B-4127-4c7d-AC8B-1B2AC737F78D.png?w=549 549w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627867275_F7ADD81B-4127-4c7d-AC8B-1B2AC737F78D.png?resize=300%2C162 300w\" sizes=\"(max-width: 549px) 100vw, 549px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u2463.\u5806\u53e0\u6761\u5f62\u56fe<\/p>\n\n\n\n<p>\u5806\u53e0\u67f1\u72b6\u56fe\u5177\u4f53\u5c55\u793a\u6bcf\u79cd\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u4e2d\u6bcf\u79cd\u7ec6\u80de\u4e9a\u7fa4\u4e2d\u4e0a\u8c03\u3001\u4e0b\u8c03\u548c\u6ca1\u6709\u7edf\u8ba1\u5b66\u5dee\u5f02\u7684\u57fa\u56e0\u96c6\u6570\u76ee\uff1b<\/p>\n\n\n\n<p>\u4e0a\u65b9\u7684\u6761\u5f62\u4ee3\u8868\u6bcf\u4e2a\u4e9a\u7fa4\u4e2d\u4e0d\u540c\u65b9\u6cd5\u4e2d\u5dee\u5f02\u7684\u57fa\u56e0\u6570\u76ee\uff0c\u7ea2\u8272\u4ee3\u8868\u4e0a\u8c03\u7684\u5dee\u5f02\u57fa\u56e0\u96c6\uff0c\u84dd\u8272\u4ee3\u8868\u4e0b\u8c03\u7684\u5dee\u5f02\u57fa\u56e0\u96c6\uff1b<\/p>\n\n\n\n<p>\u4e2d\u95f4\u7684\u67f1\u5f62\u56fe\u4ee3\u8868\u6bcf\u4e2a\u4e9a\u7fa4\u4e2d\u4e0d\u540c\u65b9\u6cd5\u4e2d\u4e0a\u8c03\u3001\u4e0b\u8c03\u548c\u6ca1\u6709\u7edf\u8ba1\u5b66\u610f\u4e49\u7684\u57fa\u56e0\u96c6\u7684\u6bd4\u4f8b\uff1b<\/p>\n\n\n\n<p>irGSEA.barplot.plot &lt;- irGSEA.barplot(object = result.dge,<\/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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;method = c(&#8220;AUCell&#8221;, &#8220;UCell&#8221;, &#8220;singscore&#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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&#8220;ssgsea&#8221;))<\/p>\n\n\n\n<p>irGSEA.barplot.plot<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"553\" height=\"273\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627905263_99ED0EEC-C689-4497-A5C6-DAD96845ADF5.png?resize=553%2C273\" alt=\"\" class=\"wp-image-61034\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627905263_99ED0EEC-C689-4497-A5C6-DAD96845ADF5.png?w=553 553w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627905263_99ED0EEC-C689-4497-A5C6-DAD96845ADF5.png?resize=300%2C148 300w\" sizes=\"(max-width: 553px) 100vw, 553px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>2\uff09. \u5c40\u90e8\u5c55\u793a<\/p>\n\n\n\n<p>\u2460.\u5bc6\u5ea6\u6563\u70b9\u56fe<\/p>\n\n\n\n<p>\u5bc6\u5ea6\u6563\u70b9\u56fe\u5c06\u57fa\u56e0\u96c6\u7684\u5bcc\u96c6\u5206\u6570\u548c\u7ec6\u80de\u4e9a\u7fa4\u5728\u4f4e\u7ef4\u7a7a\u95f4\u7684\u6295\u5f71\u7ed3\u5408\u8d77\u6765\uff0c\u5c55\u793a\u4e86\u7279\u5b9a\u57fa\u56e0\u96c6\u5728\u7a7a\u95f4\u4e0a\u7684\u8868\u8fbe\u6c34\u5e73\u3002\u5176\u4e2d\uff0c\u989c\u8272\u8d8a\u9ec4\uff0c\u4ee3\u8868\u5bcc\u96c6\u5206\u6570\u8d8a\u9ad8\uff1b<\/p>\n\n\n\n<p>scatterplot &lt;- irGSEA.density.scatterplot(object = pbmc3k.final,<\/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;method = &#8220;UCell&#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;show.geneset = &#8220;HALLMARK-INFLAMMATORY-RESPONSE&#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;reduction = &#8220;umap&#8221;)<\/p>\n\n\n\n<p>scatterplot<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"543\" height=\"341\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627939599_6002F582-02BD-489d-9CE5-F73FCEA44D5B.png?resize=543%2C341\" alt=\"\" class=\"wp-image-61035\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627939599_6002F582-02BD-489d-9CE5-F73FCEA44D5B.png?w=543 543w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728627939599_6002F582-02BD-489d-9CE5-F73FCEA44D5B.png?resize=300%2C188 300w\" sizes=\"(max-width: 543px) 100vw, 543px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u2461.\u534a\u5c0f\u63d0\u7434\u56fe<\/p>\n\n\n\n<p>\u534a\u5c0f\u63d0\u7434\u56fe\u540c\u65f6\u4ee5\u5c0f\u63d0\u7434\u56fe\uff08\u5de6\u8fb9\uff09\u548c\u7bb1\u7ebf\u56fe\uff08\u53f3\u8fb9\uff09\u8fdb\u884c\u5c55\u793a\u3002\u4e0d\u540c\u989c\u8272\u4ee3\u8868\u4e0d\u540c\u7684\u7ec6\u80de\u4e9a\u7fa4\uff1b<\/p>\n\n\n\n<p>halfvlnplot &lt;- irGSEA.halfvlnplot(object = pbmc3k.final,<\/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;&nbsp;&nbsp;&nbsp;&nbsp;method = &#8220;UCell&#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;&nbsp;&nbsp;&nbsp;&nbsp;show.geneset = &#8220;HALLMARK-INFLAMMATORY-RESPONSE&#8221;)<\/p>\n\n\n\n<p>halfvlnplot<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"546\" height=\"382\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628007101_BDF96252-48D5-4939-9C32-641CB9947E9F.png?resize=546%2C382\" alt=\"\" class=\"wp-image-61036\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628007101_BDF96252-48D5-4939-9C32-641CB9947E9F.png?w=546 546w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628007101_BDF96252-48D5-4939-9C32-641CB9947E9F.png?resize=300%2C210 300w\" sizes=\"(max-width: 546px) 100vw, 546px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u2462.\u5c71\u5ce6\u56fe<\/p>\n\n\n\n<p>\u5c71\u5ce6\u56fe\u4e2d\u4e0a\u65b9\u7684\u6838\u5bc6\u5ea6\u66f2\u7ebf\u5c55\u793a\u4e86\u6570\u636e\u7684\u4e3b\u8981\u5206\u5e03\uff0c\u4e0b\u65b9\u7684\u6761\u5f62\u7f16\u7801\u56fe\u5c55\u793a\u4e86\u7ec6\u80de\u4e9a\u7fa4\u5177\u4f53\u7684\u6570\u91cf\u3002\u4e0d\u540c\u989c\u8272\u4ee3\u8868\u4e0d\u540c\u7684\u7ec6\u80de\u4e9a\u7fa4\uff0c\u800c\u6a2a\u5750\u6807\u4ee3\u8868\u4e0d\u540c\u7684\u8868\u8fbe\u6c34\u5e73\uff1b<\/p>\n\n\n\n<p>ridgeplot &lt;- irGSEA.ridgeplot(object = pbmc3k.final,<\/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;method = &#8220;UCell&#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;show.geneset = &#8220;HALLMARK-INFLAMMATORY-RESPONSE&#8221;)<\/p>\n\n\n\n<p>ridgeplot<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"553\" height=\"381\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628052637_29314956-6EAA-4761-A0A9-987FB96C72C2.png?resize=553%2C381\" alt=\"\" class=\"wp-image-61037\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628052637_29314956-6EAA-4761-A0A9-987FB96C72C2.png?w=553 553w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628052637_29314956-6EAA-4761-A0A9-987FB96C72C2.png?resize=300%2C207 300w\" sizes=\"(max-width: 553px) 100vw, 553px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u2463.\u5bc6\u5ea6\u70ed\u56fe<\/p>\n\n\n\n<p>\u5bc6\u5ea6\u70ed\u56fe\u5c55\u793a\u4e86\u5177\u4f53\u5dee\u5f02\u57fa\u56e0\u5728\u4e0d\u540c\u7ec6\u80de\u4e9a\u7fa4\u4e2d\u7684\u8868\u8fbe\u548c\u5206\u5e03\u6c34\u5e73\u3002\u989c\u8272\u8d8a\u7ea2\uff0c\u4ee3\u8868\u5bcc\u96c6\u5206\u6570\u8d8a\u9ad8\uff1b<\/p>\n\n\n\n<p>densityheatmap &lt;- irGSEA.densityheatmap(object = pbmc3k.final,<\/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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;method = &#8220;UCell&#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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;show.geneset = &#8220;HALLMARK-INFLAMMATORY-RESPONSE&#8221;)<\/p>\n\n\n\n<p>densityheatmap<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"550\" height=\"437\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628086094_42949A68-91D5-440f-962F-273042236D99.png?resize=550%2C437\" alt=\"\" class=\"wp-image-61038\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628086094_42949A68-91D5-440f-962F-273042236D99.png?w=550 550w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1728628086094_42949A68-91D5-440f-962F-273042236D99.png?resize=300%2C238 300w\" sizes=\"(max-width: 550px) 100vw, 550px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p><strong>\u5c0f\u7ed3<\/strong><strong><\/strong><\/p>\n\n\n\n<p>irGSEA \u7684 R \u5305\u5408\u5e76\u6240\u6709\u516d\u79cd\u65b9\u6cd5\u7684\u7ed3\u679c\uff0c\u901a\u8fc7\u91c7\u7528\u7a33\u5065\u7684 RRA \u6765\u786e\u5b9a\u76ee\u6807\u57fa\u56e0\u96c6\u5728\u4e0d\u540c\u8bc4\u5206\u65b9\u6cd5\u4e2d\u7684\u7edf\u8ba1\u663e\u7740\u6027\u3002irGSEA\u4f18\u5148\u8003\u8651\u7528\u6237\u53cb\u597d\u6027\uff0c\u5141\u8bb8\u76f4\u63a5\u8f93\u5165\u8868\u8fbe\u5f0f\u77e9\u9635\u6216\u4e0eSeurat\u5bf9\u8c61\u65e0\u7f1d\u4ea4\u4e92\u3002\u6b64\u5916\uff0cirGSEA\u96c6\u6210\u4e86\u51e0\u79cd\u7528\u6237\u53cb\u597d\u7684\u53ef\u89c6\u5316\u5de5\u5177\u6765\u663e\u793a\u7ed3\u679c\u3002\u662f\u4e0d\u662f\u7528\u8d77\u6765\u65b9\u4fbf\u591a\u4e86\uff1f\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\u4e5f\u66f4\u51c6\u786e\u4e86\uff1f\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u5feb\u6765\u5b66\u4e60\u5427\uff01\u5927\u6d77\u7684\u7684\u5206\u4eab\u5230\u6b64\u7ed3\u675f\u5566\uff01\u4e0d\u8fc7\u8fd8\u662f\u8981\u7ed9\u5927\u5bb6\u5c0f\u9001\u4e00\u6ce2\u798f\u5229\uff01\u5927\u6d77\u54e5\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u4e91\u5de5\u5177\uff01\u540c\u5b66\u4eec\u5982\u679c\u89c9\u5f97\u81ea\u5df1\u7684\u4ee3\u7801\u6c34\u5e73\u4e00\u822c\uff0c\u5bf9\u4e8e\u5f88\u591a\u7684\u53c2\u6570\u4e0d\u77e5\u9053\u600e\u4e48\u6539\uff0c\u53ef\u4ee5\u4f53\u9a8c\u4e00\u4e0b\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177\uff0c\u53ea\u9700\u8f93\u5165\u6570\u636e\uff0c\u5373\u53ef\u8f7b\u677e\u751f\u6210\u6240\u9700\u56fe\u8868\uff0c\u5b57\u4f53\u5927\u5c0f\u3001\u6807\u9898\u7b49\u4e5f\u53ef\u4e00\u952e\u66f4\u6539\u3002\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53bb\u4e91\u751f\u4fe1\uff08http:\/\/www.biocloudservice.com\/home.html\uff09\u4f53\u9a8c\u4e00\u4e0b\u5427\uff01<\/p>\n\n\n\n<p><strong>\u53c2\u8003\u6587\u732e<\/strong><strong><\/strong><\/p>\n\n\n\n<ul>\n<li><strong><em><strong><em>Chuiqin Fan, Fuyi Chen, Yuanguo Chen, Liangping Huang, Manna Wang, Yulin Liu, Yu Wang, Huijie Guo, Nanpeng Zheng, Yanbing Liu, Hongwu Wang, Lian Ma, irGSEA: the integration of single-cell rank-based gene set enrichment analysis, Briefings in Bioinformatics, Volume 25, Issue 4, July 2024, bbae243, <\/em><\/strong><\/em><\/strong><a href=\"https:\/\/doi.org\/10.1093\/bib\/bbae243\"><strong><em><u><strong><em>https:\/\/doi.org\/10.1093\/bib\/bbae243<\/em><\/strong><\/u><\/em><\/strong><\/a><strong><em><strong><em><\/em><\/strong><\/em><\/strong><\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u524d\u8a00 \u5c0f\u4f19\u4f34\u4eec\u90fd\u8d8b\u5411\u4e8e\u4f7f\u7528\u672a\u6821\u6b63\u6279\u6b21\u6548\u5e94\u540e\u7684\u6570\u636e\u8fdb\u884c\u5dee\u5f02\u57fa\u56e0\u5206\u6790\uff0c\u4f46\u662f\u5728\u5bcc\u96c6\u5206\u6790\u7684\u8fc7\u7a0b\u4e2d\uff0c\u4f7f\u7528\u6821\u6b63\u540e\u7684\u6570\u636e\u8fd8\u662f [&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\/61028"}],"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=61028"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61028\/revisions"}],"predecessor-version":[{"id":61039,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61028\/revisions\/61039"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61028"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61028"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61028"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}