{"id":56180,"date":"2024-06-16T17:30:22","date_gmt":"2024-06-16T09:30:22","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=56180"},"modified":"2024-06-16T17:30:22","modified_gmt":"2024-06-16T09:30:22","slug":"scmerge2%e9%ad%94%e6%b3%95%e6%8c%87%e5%8d%97%ef%bc%9a%e5%b0%8f%e6%9e%9c%e5%b8%a6%e4%bd%a0%e9%a2%86%e7%95%a5%e5%8d%95%e7%bb%86%e8%83%9e%e6%95%b0%e6%8d%ae%e8%9e%8d%e5%90%88%e7%9a%84%e5%a5%87%e5%a6%99-3","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=56180","title":{"rendered":"scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01"},"content":{"rendered":"


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href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><\/p>\n<\/div>\n<section data-mpa-powered-by=\"yiban.io\"><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014479\" data-ratio=\"0.23333333333333334\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/1_rE2v0O5WiaUDJjgv5bxK2G1ePHyH2g.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"letter-spacing: 0.578px;text-wrap: wrap;font-family: \u5b8b\u4f53;font-size: 15px;text-align: center;\">\u524d\u8a00<\/strong><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u5355\u7ec6\u80de\u591a\u6837\u672c\u6574\u5408\u5de5\u5177\u5927\u5bb6\u4e5f\u5b66\u8fc7\u5f88\u591a\u4e86\u5427\uff01\u4f46\u662f\u9664\u4e86 Seurat\u3001SAUCIE \u548c Scanorama \u4e4b\u5916\uff0c\u5176\u4ed6\u51e0\u79cd\u5feb\u901f\u7a0b\u5e8f\uff08deepMNN\u3001BBKNN\u3001Harmony\u3001scVI\u3001scANVI \u548c 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scMerge2\u5e94\u8fd0\u800c\u751f\uff0c\u8fd9\u662f\u4e00\u79cd\u53ef\u6269\u5c55\u7684\u9ad8\u5bb9\u91cf\u7b97\u6cd5\uff0c\u53ef\u5bf9\u56fe\u96c6\u89c4\u6a21\u7684\u591a\u6837\u672c\u591a\u6761\u4ef6\u5355\u7ec6\u80de\u7814\u7a76\u8fdb\u884c\u6570\u636e\u6574\u5408\u3002\u4e0b\u9762\u8ddf\u7740\u5c0f\u679c\u6765\u5b66\u4e60\u4e00\u4e0b\u5427\uff01<\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>scMerge2\u4ecb\u7ecd<\/strong><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 15px;\">scMerge \u7b97\u6cd5\u53ef\u53bb\u9664\u6279\u6b21\u6548\u5e94\uff0c\u5e76\u5bf9\u5355\u7ec6\u80de RNA-Seq \u6570\u636e\u8fdb\u884c\u5f52\u4e00\u5316\u5904\u7406\u3002\u5b83\u7531\u4e09\u4e2a\u5173\u952e\u90e8\u5206\u7ec4\u6210\uff0c\u5305\u62ec<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u2022 \u786e\u5b9a\u7a33\u5b9a\u8868\u8fbe\u57fa\u56e0\uff08SEG\uff09\u4f5c\u4e3a “\u9634\u6027\u5bf9\u7167”\uff0c\u4ee5\u4f30\u8ba1\u4e0d\u9700\u8981\u7684\u56e0\u7d20\uff1b<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u2022 \u6784\u5efa\u4f2a\u91cd\u590d\uff0c\u4ee5\u4f30\u8ba1\u4e0d\u9700\u8981\u7684\u56e0\u7d20\u7684\u5f71\u54cd\uff1b<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u2022 \u4f7f\u7528\u5feb\u901f RUVIII \u6a21\u578b\u8c03\u6574\u5b58\u5728\u4e0d\u5fc5\u8981\u53d8\u5f02\u7684\u6570\u636e\u96c6\u3002<\/span>    <\/span><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014379\" data-ratio=\"0.9864864864864865\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_E7uAS1ueBF8p6c2eeNICjzsEaJlNKQ.jpg?resize=553%2C545\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSBmc6icsaELKbybeCHtmUfCuWOE7uAS1ueBF8p6c2eeNICjzsEaJlNKQ\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"666\" height=\"545 .8800048828125\" width=\"553 .2100219726562\" data-recalc-dims=\"1\"><\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>scMerge2\u793a\u4f8b<\/strong><\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>\u5b89\u88c5R\u5305<\/strong><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 15px;\">scMerge\u53ef\u5728bioconductor \uff08https:\/\/bioconductor.org\/packages\/scMerge\uff09 \u4e0a\u4f7f\u7528\u3002\u60a8\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u65b9\u6cd5\u5b89\u88c5\u5b83\uff1a<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u4ece Bioconductor \u5b89\u88c5 scMerge\uff0c\u9700\u8981 R 3.6.0 \u6216\u4ee5\u4e0a\u7248\u672c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::<span class=\"code-snippet__keyword\">install<\/span>(<span class=\"code-snippet__string\">\"scMerge\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##\u60a8\u4e5f\u53ef\u4ee5\u5c1d\u8bd5\u5b89\u88c5 ScMerge \u7684 Bioconductor \u5f00\u53d1\u7248<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::<span class=\"code-snippet__keyword\">install<\/span>(<span class=\"code-snippet__string\">\"scMerge\"<\/span>, <span class=\"code-snippet__keyword\">version<\/span> = <span class=\"code-snippet__string\">\"devel\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><o:page><\/o:page><\/section>\n<section><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>\u52a0\u8f7d\u5305\u548c\u6570\u636e<\/strong><\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\"><code><span class=\"code-snippet_outer\">suppressPackageStartupMessages({<\/span><\/code><code><span class=\"code-snippet_outer\"> library(SingleCellExperiment)<\/span><\/code><code><span class=\"code-snippet_outer\"> library(scMerge)<\/span><\/code><code><span class=\"code-snippet_outer\"> library(scater)<\/span><\/code><code><span class=\"code-snippet_outer\">})<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u6211\u4eec\u5728R\u5305\u4e2d\u63d0\u4f9b\u4e86\u4e00\u4e2a\u5c0f\u9f20\u80da\u80ce\u5e72\u7ec6\u80de\uff08mESC\uff09\u6570\u636e\u793a\u4f8b\uff0c\u4ee5\u53ca\u4e00\u7ec4\u9884\u5148\u8ba1\u7b97\u597d\u7684\u7a33\u5b9a\u8868\u8fbe\u57fa\u56e0\uff08SEG\uff09\u5217\u8868\uff0c\u7528\u4f5c\u9634\u6027\u5bf9\u7167\u57fa\u56e0\u3002<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u5b8c\u6574\u7684\u3001\u672a\u7ecf\u89c4\u8303\u5316\u7684 mESC \u6570\u636e\u53ef\u5728\u8fd9\u91cc\u627e\u5230<\/span><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\uff08<\/span><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;\">https:\/\/www.maths.usyd.edu.au\/u\/yingxinl\/wwwnb\/scMergeData\/sce_mESC.rda<\/span><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\uff09<\/span><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">R\u5305\u9644\u5e26\u4e86\u8be5\u6570\u636e\u7684\u5b50\u6837\u672c\u3001\u4e24\u4e2a\u6279\u6b21\u7248\u672c\uff08\u547d\u540d\u4e3a\u201cbatch2\u201d\u548c\u201cbatch3\u201d\uff0c\u4ee5\u4fbf\u4e0e\u5b8c\u6574\u6570\u636e\u4fdd\u6301\u4e00\u81f4\uff09\u3002<\/span><\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"kotlin\"><code><span class=\"code-snippet_outer\">## \u5c0f\u9f20 ESC \u6570\u636e\u5b50\u96c6<\/span><\/code><code><span class=\"code-snippet_outer\">data(\"example_sce\", package = \"scMerge\")<\/span><\/code><code><span class=\"code-snippet_outer\">data(\"segList_ensemblGeneID\", package = \"scMerge\")<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u8fd9\u4e2a mESC \u6570\u636e\u4e2d\uff0c\u6211\u4eec\u6c47\u96c6\u4e86\u6765\u81ea\u4e09\u79cd\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u7684\u4e24\u4e2a\u4e0d\u540c\u6279\u6b21\u7684\u6570\u636e\u3002\u901a\u8fc7 PCA \u56fe\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u5c3d\u7ba1\u7ec6\u80de\u7c7b\u578b\u6709\u5f88\u5f3a\u7684\u5206\u79bb\u6027\uff0c\u4f46\u6279\u6b21\u6548\u5e94\u4e5f\u9020\u6210\u4e86\u5f88\u5f3a\u7684\u5206\u79bb\u6027\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code><span class=\"code-snippet_outer\">example_sce = runPCA(example_sce, exprs_values = \"logcounts\")<\/span><\/code><code><span class=\"code-snippet_outer\">scater::plotPCA(example_sce,<\/span><\/code><code><span class=\"code-snippet_outer\"> colour_by = \"cellTypes\",<\/span><\/code><code><span class=\"code-snippet_outer\"> shape_by = \"batch\")<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><\/span><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014376\" data-ratio=\"0.6175925925925926\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/3_n3DCTdXBqlkDvG7toquSE94ddBHQWQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVS9iciasgIgSqWgphuUERVIWVudCn3DCTdXBqlkDvG7toquSE94ddBHQWQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"342.4100036621094\" width=\"553.6099853515625\"><\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>\u65e0\u76d1\u7763 scMerge2<\/strong><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u65e0\u76d1\u7763\u60c5\u51b5\u4e0b\uff0c\u6211\u4eec\u5c06\u5bf9\u6bcf\u4e2a\u6279\u6b21\u4e2d\u7684\u5171\u4eab\u8fd1\u90bb\u56fe\u8fdb\u884c\u56fe\u805a\u7c7b\uff0c\u4ee5\u83b7\u5f97\u4f2a\u526f\u672c\u3002\u8fd9\u9700\u8981\u7528\u6237\u63d0\u4f9b\u4e00\u4e2a\u5411\u91cf\uff0c\u5176\u4e2d\u5305\u542b\u6bcf\u4e2a\u6279\u6b21\u4e2d\u6784\u5efa\u6700\u8fd1\u90bb\u56fe\u65f6\u7684\u90bb\u56fe\u6570\u91cf\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u4e3a10\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),<\/span><\/code><code><span class=\"code-snippet_outer\"> batch = example_sce$batch,<\/span><\/code><code><span class=\"code-snippet_outer\"> ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">assay(example_sce, \"scMerge2\") <- scMerge2_res$newY<\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(2022)<\/span><\/code><code><span class=\"code-snippet_outer\">example_sce <- scater::runPCA(example_sce, exprs_values = 'scMerge2') <\/span><\/code><code><span class=\"code-snippet_outer\">scater::plotPCA(example_sce, colour_by = 'cellTypes', shape = 'batch')<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><\/span><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014378\" data-ratio=\"0.6175925925925926\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_Q3KJMR1wwcF9qcfvrnEXH52ZW3Hs8Q.png?resize=553%2C342\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/8_Q3KJMR1wwcF9qcfvrnEXH52ZW3Hs8Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVST9u1BhE6YWucDVxcIgGBSmxIQ3KJMR1wwcF9qcfvrnEXH52ZW3Hs8Q\/640?wx_fmt=png''\" data-type=\"png\" data-w=\"1080\" height=\"342 .4100036621094\" width=\"553 .6099853515625\" data-recalc-dims=\"1\"><\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>\u534a\u76d1\u7763scMerge2<\/strong><\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),<\/span><\/code><code><span class=\"code-snippet_outer\"> batch = example_sce$batch,<\/span><\/code><code><span class=\"code-snippet_outer\"> cellTypes = example_sce$cellTypes,<\/span><\/code><code><span class=\"code-snippet_outer\"> ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">assay(example_sce, \"scMerge2\") <- scMerge2_res$newY<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">example_sce = scater::runPCA(example_sce, exprs_values = 'scMerge2') <\/span><\/code><code><span class=\"code-snippet_outer\">scater::plotPCA(example_sce, colour_by = 'cellTypes', shape = 'batch')<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><\/span><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014377\" data-ratio=\"0.6175925925925926\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/5_gC0B1WtxFdmzGO3BibgdfoI78uZStg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSUbduRqRZhaUKARwQIoic5UeB8cgC0B1WtxFdmzGO3BibgdfoI78uZStg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"342.4100036621094\" width=\"553.6099853515625\"><\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>scMerge2 \u7684\u66f4\u591a\u8be6\u7ec6\u4fe1\u606f<\/strong><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u6bcf\u4e2a\u5355\u5143\u683c\u5206\u7ec4\u5185\u6784\u5efa\u7684\u4f2a\u5757\u6570\u91cf\u9ed8\u8ba4\u8bbe\u7f6e\u4e3a 30\u3002\u6570\u5b57\u8d8a\u5927\uff0c\u6a21\u578b\u4f30\u7b97\u4e2d\u7684\u4f2a\u5757\u6570\u636e\u5c31\u8d8a\u591a\uff0c\u4f30\u7b97\u65f6\u95f4\u4e5f\u5c31\u8d8a\u957f\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),<\/span><\/code><code><span class=\"code-snippet_outer\"> batch = example_sce$batch,<\/span><\/code><code><span class=\"code-snippet_outer\"> ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/span><\/code><code><span class=\"code-snippet_outer\"> k_pseudoBulk = 50,<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">assay(example_sce, \"scMerge2\") <- scMerge2_res$newY<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(2022)<\/span><\/code><code><span class=\"code-snippet_outer\">example_sce <- scater::runPCA(example_sce, exprs_values = 'scMerge2') <\/span><\/code><code><span class=\"code-snippet_outer\">scater::plotPCA(example_sce, colour_by = 'cellTypes', shape = 'batch')<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><\/span><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014380\" data-ratio=\"0.6175925925925926\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_I89aibs3Z4dol84Qnfezvou6WX4G9w.png?resize=553%2C342\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSrKfwjBNfZ9kMYKbroH9b55ZloI89aibs3Z4dol84Qnfezvou6WX4G9w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"342 .4100036621094\" width=\"553 .6099853515625\" data-recalc-dims=\"1\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014484\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/7_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"letter-spacing: 0.578px;text-wrap: wrap;color: rgb(34, 34, 38);font-family: "Times New Roman";font-size: 15px;font-weight: 700;background-color: rgb(255, 255, 255);text-align: center;\">\u5728\u5904\u7406\u5927\u91cf\u6570\u636e\u65f6\uff0c\u6211\u4eec\u53ef\u4ee5\u6bcf\u6b21\u83b7\u53d6\u8f83\u5c0f\u5355\u5143\u683c\u5b50\u96c6\u7684\u8c03\u6574\u540e\u77e9\u9635\u3002\u8fd9\u53ef\u4ee5\u901a\u8fc7\u5728in\u51fd\u6570\u4e2d\u8bbe\u7f6e\uff0c\u51fd\u6570\u5c06\u4e0d\u8fd4\u56de\u8c03\u6574\u540e\u7684\u6574\u4e2a\u77e9\u9635\uff0c\u800c\u662f\u8f93\u51fa\u4f30\u8ba1\u503c\u3002\u7136\u540e\uff0c\u4e3a\u4e86\u4f7f\u7528\u4f30\u8ba1\u503c\u5f97\u5230\u8c03\u6574\u540e\u7684\u77e9\u9635\uff0c\u6211\u4eec\u9996\u5148\u9700\u8981\u5bf9\u5bf9\u6570\u77e9\u9635\u8fdb\u884c\u4f59\u5f26\u5f52\u4e00\u5316\u5904\u7406\uff0c\u7136\u540e\u8ba1\u7b97\u4f59\u5f26\u5f52\u4e00\u5316\u77e9\u9635\u7684\u884c\u5411\uff08\u57fa\u56e0\u5411\uff09\u5e73\u5747\u503c\uff08\u8fd9\u662f\u56e0\u4e3a\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u5728\u6b65\u9aa4\u4e4b\u524d\u4f1a\u5bf9\u5bf9\u6570\u5f52\u4e00\u5316\u77e9\u9635\u8fdb\u884c\u4f59\u5f26\u5f52\u4e00\u5316\u5904\u7406\uff09\u3002\u7136\u540e\uff0c\u6bcf\u6b21\u6211\u4eec\u90fd\u53ef\u4ee5\u7528\u5b83\u6765\u8c03\u6574\u5355\u5143\u683c\u5b50\u96c6\u7684\u77e9\u9635\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),<\/span><\/code><code><span class=\"code-snippet_outer\"> batch = example_sce$batch,<\/span><\/code><code><span class=\"code-snippet_outer\"> ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE,<\/span><\/code><code><span class=\"code-snippet_outer\"> return_matrix = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">cosineNorm_mat <- batchelor::cosineNorm(logcounts(example_sce))<\/span><\/code><code><span class=\"code-snippet_outer\">adjusted_means <- DelayedMatrixStats::rowMeans2(cosineNorm_mat)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">newY <- list()<\/span><\/code><code><span class=\"code-snippet_outer\">for (i in levels(example_sce$batch)) {<\/span><\/code><code><span class=\"code-snippet_outer\"> newY[[i]] <- getAdjustedMat(cosineNorm_mat[, example_sce$batch == i],<\/span><\/code><code><span class=\"code-snippet_outer\"> scMerge2_res$fullalpha,<\/span><\/code><code><span class=\"code-snippet_outer\"> ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/span><\/code><code><span class=\"code-snippet_outer\"> ruvK = 20,<\/span><\/code><code><span class=\"code-snippet_outer\"> adjusted_means = adjusted_means)<\/span><\/code><code><span class=\"code-snippet_outer\">} <\/span><\/code><code><span class=\"code-snippet_outer\">newY <- do.call(cbind, newY)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">assay(example_sce, \"scMerge2\") <- newY[, colnames(example_sce)]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(2022)<\/span><\/code><code><span class=\"code-snippet_outer\">example_sce <- scater::runPCA(example_sce, exprs_values = 'scMerge2') <\/span><\/code><code><span class=\"code-snippet_outer\">scater::plotPCA(example_sce, colour_by = 'cellTypes', shape = 'batch')<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014381\" data-ratio=\"0.6175925925925926\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_Q3KJMR1wwcF9qcfvrnEXH52ZW3Hs8Q.png?resize=553%2C342\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/8_Q3KJMR1wwcF9qcfvrnEXH52ZW3Hs8Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVST9u1BhE6YWucDVxcIgGBSmxIQ3KJMR1wwcF9qcfvrnEXH52ZW3Hs8Q\/640?wx_fmt=png''\" data-type=\"png\" data-w=\"1080\" height=\"342 .4100341796875\" width=\"553 .6099853515625\" data-recalc-dims=\"1\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">scMerge2 \u4e3a\u9700\u8981\u901a\u8fc7\u51fd\u6570\u8fdb\u884c\u591a\u7ea7\u8c03\u6574\u7684\u6570\u636e\u6574\u5408\u63d0\u4f9b\u4e86\u5206\u7ea7\u5408\u5e76\u7b56\u7565\u3002\u4f8b\u5982\uff0c\u5bf9\u4e8e\u6709\u591a\u4e2a\u6837\u672c\u7684\u6570\u636e\u96c6\uff0c\u6211\u4eec\u53ef\u80fd\u5e0c\u671b\u5148\u6d88\u9664\u6570\u636e\u96c6\u5185\u90e8\u7684\u6837\u672c\u6548\u5e94\uff0c\u7136\u540e\u518d\u4e0e\u5176\u4ed6\u6570\u636e\u96c6\u6574\u5408\u3002\u4e0b\u9762\uff0c\u6211\u4eec\u5c06\u8bf4\u660e\u5982\u4f55\u5efa\u7acb\u5206\u5c42\u5408\u5e76\u987a\u5e8f\uff0c\u4f5c\u4e3ascMerge2h()scMerge2h() \u7684\u8f93\u5165\u3002<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u4e3a\u4e86\u4fbf\u4e8e\u8bf4\u660e\uff0c\u6211\u9996\u5148\u4e3a\u6837\u672c\u6570\u636e\u521b\u5efa\u4e86\u4e00\u4e2a\u5047\u6837\u672c\u4fe1\u606f\u3002\u73b0\u5728\uff0c\u6bcf\u4e2a\u6279\u6b21\u90fd\u6709\u4e24\u4e2a\u6837\u672c\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\"># \u521b\u5efa\u4e00\u4e2a\u5047\u6837\u672c\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">example_sce$sample <- rep(c(1:4), each = 50)<\/span><\/code><code><span class=\"code-snippet_outer\">table(example_sce$sample, example_sce$batch)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u8981\u6267\u884c\u5408\u5e76\uff0c\u6211\u4eec\u9700\u8981\u521b\u5efa\u4e00\u4e2a\u5206\u5c42\u7d22\u5f15\u5217\u8868scMerge2h<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">1.\u4e00\u4e2a\u5206\u5c42\u7d22\u5f15\u5217\u8868\uff0c\u8868\u793a\u8981\u5408\u5e76\u7684\u5355\u5143\u683c\u7684\u7d22\u5f15\uff1b<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">2.\u4e00\u4e2a\u6279\u6b21\u4fe1\u606f\u5217\u8868\uff0c\u8868\u793a\u6bcf\u6b21\u5408\u5e76\u7684\u6279\u6b21\u4fe1\u606f\u3002<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>\u573a\u666f1    <\/strong><\/span><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u6211\u4eec\u5c06\u9996\u5148\u8bf4\u660e\u4e24\u7ea7\u5408\u5e76\u7684\u60c5\u51b5\uff0c\u5176\u4e2d\u7b2c\u4e00\u7ea7\u662f\u6307\u5728\u6bcf\u4e00\u6279\u4e2d\u53bb\u9664\u6837\u672c\u6548\u5e94\uff0c\u7b2c\u4e8c\u7ea7\u662f\u6307\u4e24\u6279\u7684\u5408\u5e76\u3002<\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u9996\u5148\uff0c\u6211\u4eec\u5c06\u6784\u5efa\u5206\u5c42\u7d22\u5f15\u5217\u8868\u3002\u5206\u5c42\u7d22\u5f15\u5217\u8868\u662f\u4e00\u4e2a\u5217\u8868\uff0c\u5b83\u6307\u51fa\u4e86\u6bcf\u4e00\u5c42\u4e2d\u54ea\u4e9b\u5355\u5143\u683c\u7684\u7d22\u5f15\u8981\u8fdb\u884c\u5408\u5e76\u3002\u5217\u8868\u5143\u7d20\u7684\u6570\u91cf\u5e94\u4e0e\u5408\u5e76\u5c42\u7ea7\u7684\u6570\u91cf\u76f8\u540c\u3002\u5bf9\u4e8e\u6bcf\u4e2a\u5143\u7d20\uff0c\u5b83\u5e94\u5305\u542b\u6bcf\u4e2a\u5408\u5e76\u5355\u5143\u7684\u7d22\u5f15\u5411\u91cf\u5217\u8868\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\"># \u6784\u5efa\u5206\u5c42\u7d22\u5f15\u5217\u8868<\/span><\/code><code><span class=\"code-snippet_outer\">h_idx_list <- list(level1 = split(seq_len(ncol(example_sce)), example_sce$batch),<\/span><\/code><code><span class=\"code-snippet_outer\"> level2 = list(seq_len(ncol(example_sce))))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u7b2c 1 \u5c42\uff0c\u6211\u4eec\u5c06\u6267\u884c\u4e24\u6b21\u5408\u5e76\uff0c\u6bcf\u4e00\u6279\u5408\u5e76\u4e00\u6b21\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u6709\u4e00\u4e2a\u7531\u4e24\u4e2a\u7d22\u5f15\u5411\u91cf\u7ec4\u6210\u7684\u5217\u8868\u3002\u6bcf\u4e2a\u77e2\u91cf\u8868\u793a\u5404\u6279\u6b21\u5355\u5143\u683c\u7684\u7d22\u5f15\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\">h_idx_list$level1<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014385\" data-ratio=\"0.46965699208443273\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_3Jt5SNpCjGyvhd9CC2g63icB1NZxUA.jpg?resize=553%2C260\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSBexUnqFicS1MEoBQZlznDT5ULt3Jt5SNpCjGyvhd9CC2g63icB1NZxUA\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"758\" height=\"260 .0\" width=\"553 .6099853515625\" data-recalc-dims=\"1\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u7b2c 2 \u5c42\uff0c\u6211\u4eec\u5c06\u6267\u884c\u4e00\u6b21\u5408\u5e76\uff0c\u5408\u5e76\u4e24\u6279\u6570\u636e\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u6709\u4e00\u4e2a\u7d22\u5f15\u5411\u91cf\u5217\u8868\uff0c\u8868\u793a\u5b8c\u6574\u6570\u636e\u4e2d\u6240\u6709\u5355\u5143\u683c\u7684\u7d22\u5f15\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\">h_idx_list$level2<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><\/span><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014383\" data-ratio=\"0.4029451137884873\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_3VgCC3ibWvibEWuedYdm4cU1KODBcA.jpg?resize=553%2C223\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSHCP8HEwiceIFZjDL0Me0lGevianB3VgCC3ibWvibEWuedYdm4cU1KODBcA\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"747\" height=\"223 .20001220703125\" width=\"553 .6099853515625\" data-recalc-dims=\"1\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u9700\u8981\u521b\u5efa\u6279\u6b21\u4fe1\u606f\u5217\u8868\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u6784\u5efa\u6279\u6b21\u4fe1\u606f\u5217\u8868<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">batch_list <- <span class=\"code-snippet__keyword\">list<\/span>(level1 = split(example_sce$sample, example_sce$batch),<\/span><\/code><code><span class=\"code-snippet_outer\"> level2 = <span class=\"code-snippet__keyword\">list<\/span>(example_sce$batch))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-size: 15px;text-indent: 0em;letter-spacing: 0.034em;\">\u6211\u4eec\u53ef\u4ee5\u770b\u5230\u6807\u6709\u5408\u5e76\u7ea7\u522b\u7684batch_list\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\">batch_list$level1<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014382\" data-ratio=\"0.2751322751322751\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_OiaWV9olEq06nh3pLedNEOEeae1BCg.jpg?resize=553%2C152\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVS0IJwK2GtYiaP2icibHVlrhFPXFh9OiaWV9olEq06nh3pLedNEOEeae1BCg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"756\" height=\"152 .0\" width=\"553 .6099853515625\" data-recalc-dims=\"1\"><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u73b0\u5728\uff0c\u6211\u4eec\u53ef\u4ee5\u8f93\u5165and\u6765\u5206\u5c42\u5408\u5e76\u6570\u636e\u3002\u6211\u4eec\u8fd8\u9700\u8981\u8f93\u5165 a \uff0c\u5b83\u662f\u6bcf\u4e2a\u5408\u5e76\u5c42\u7ea7\u7684\u65e0\u7528\u53d8\u5f02\u6570\uff08RUV \u6a21\u578b\u4e2d\u4e3a k\uff09\u7684\u5411\u91cf\u3002\u6211\u4eec\u5efa\u8bae\u5728\u7b2c\u4e00\u5c42\u8f93\u5165\u8f83\u4f4e\u7684\u3002\u5728\u8fd9\u91cc\uff0c\u6211\u4eec\u5c06 RUV \u7684 k \u8bbe\u7f6e\u4e3a\u7b2c\u4e00\u5c42\u4e3a 2\uff0c\u7b2c\u4e8c\u5c42\u4e3a 5\u3002<\/span><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\"><\/span><\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"ini\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">batch_listh_idx_listscMerge2hruvK_listruvKruvK_list<\/span> = c(<span class=\"code-snippet__number\">2<\/span>, <span class=\"code-snippet__number\">5<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;\"><\/span><\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code><span class=\"code-snippet_outer\">scMerge2_res <- scMerge2h(exprsMat = logcounts(example_sce),<\/span><\/code><code><span class=\"code-snippet_outer\"> batch_list = batch_list,<\/span><\/code><code><span class=\"code-snippet_outer\"> h_idx_list = h_idx_list,<\/span><\/code><code><span class=\"code-snippet_outer\"> ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/span><\/code><code><span class=\"code-snippet_outer\"> ruvK_list = c(2, 5),<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">scMerge2h \u7684\u8f93\u51fa\u662f\u4e00\u4e2a\u77e9\u9635\u5217\u8868\uff0c\u663e\u793a\u6bcf\u4e00\u7ea7\u8c03\u6574\u540e\u7684\u77e9\u9635\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\">length(scMerge2_res)<\/span><\/code><code><span class=\"code-snippet_outer\">lapply(scMerge2_res, dim)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u6b64\uff0c\u6211\u4eec\u5c06\u4f7f\u7528\u4e0a\u4e00\u7ea7\u7684\u8c03\u6574\u77e9\u9635\u4f5c\u4e3a\u6700\u7ec8\u8c03\u6574\u77e9\u9635\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">assay(example_sce, \"scMerge2\") <- scMerge2_res[[length(h_idx_list)]]<\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(2022)<\/span><\/code><code><span class=\"code-snippet_outer\">example_sce <- scater::runPCA(example_sce, exprs_values = 'scMerge2') <\/span><\/code><code><span class=\"code-snippet_outer\">scater::plotPCA(example_sce, colour_by = 'cellTypes', shape = 'batch')<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014384\" data-ratio=\"0.6175925925925926\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/12_4VjF0hy5ib9ZjHpZwSXgwDEiblUMGQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSQelJRsIKiaLicxOnricPkH96icD8Ew4VjF0hy5ib9ZjHpZwSXgwDEiblUMGQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"342.4100341796875\" width=\"553.6099853515625\" \/><\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);color: rgb(2, 30, 170);font-size: 15px;\"><strong>\u573a\u666f2<\/strong><\/span><br \/><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">scMerge2h \u53ef\u4ee5\u5904\u7406\u7075\u6d3b\u7684\u5408\u5e76\u7b56\u7565\u8f93\u5165\u3002\u4f8b\u5982\uff0c\u5728\u4e0a\u8ff0\u7b2c 1 \u5c42\uff0c\u6211\u4eec\u53ea\u80fd\u5408\u5e76\u4e00\u4e2a\u6279\u6b21\u7684\u6570\u636e\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u4ece\u4fee\u6539\u6279\u6b21\u7d22\u5f15\u5217\u8868\u548c\u5206\u5c42\u7d22\u5f15\u5217\u8868\u5f00\u59cb\uff0c\u5220\u9664\u7b2c 1 \u5c42\u7684\u7b2c 2 \u6279\u5217\u8868\u3002<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">h_idx_list2 <- h_idx_list<\/span><\/code><code><span class=\"code-snippet_outer\">batch_list2 <- batch_list<\/span><\/code><code><span class=\"code-snippet_outer\">h_idx_list2$level1$batch2 <- NULL<\/span><\/code><code><span class=\"code-snippet_outer\">batch_list2$level1$batch2 <- NULL<\/span><\/code><code><span class=\"code-snippet_outer\">print(h_idx_list2)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014386\" data-ratio=\"0.7420212765957447\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/13_A6dawqhZknkpWYbWkJiakYQ3hGrGqg.jpg?resize=553%2C410\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVS85MibOPDjQtJeAueJ0Y5afZdDQA6dawqhZknkpWYbWkJiakYQ3hGrGqg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"752\" height=\"410 .6700134277344\" width=\"553 .8099975585938\" data-recalc-dims=\"1\" \/><\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\">print(batch_list2)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-croporisrc=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/14_JlhSdbfXricS1n08eyxwrwpAJrdkhA.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVS2TRY3k7OqMgkRJnFpl4lpwqp6JlhSdbfXricS1n08eyxwrwpAJrdkhA\/640?wx_fmt=jpeg'\" data-cropx1=\"0\" data-cropx2=\"813\" data-cropy1=\"49.895306859205775\" data-cropy2=\"770.442238267148\" data-imgfileid=\"100014387\" data-ratio=\"0.8880688806888068\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_Cib8suricUxTPZbr3QuAfGCPUKAiag.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSCIoqV40cDuiaGt8YplnWTDXqOKjpCib8suricUxTPZbr3QuAfGCPUKAiag\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"813\" style=\"width: 554px;height: 491px;\" data-recalc-dims=\"1\" \/><\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">scMerge2_res <- scMerge2h(exprsMat = logcounts(example_sce),<\/span><\/code><code><span class=\"code-snippet_outer\"> batch_list = batch_list2,<\/span><\/code><code><span class=\"code-snippet_outer\"> h_idx_list = h_idx_list2,<\/span><\/code><code><span class=\"code-snippet_outer\"> ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/span><\/code><code><span class=\"code-snippet_outer\"> ruvK_list = c(2, 5),<\/span><\/code><code><span class=\"code-snippet_outer\"> verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">assay(example_sce, \"scMerge2\") <- scMerge2_res[[length(h_idx_list)]]<\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(2022)<\/span><\/code><code><span class=\"code-snippet_outer\">example_sce <- scater::runPCA(example_sce, exprs_values = 'scMerge2') <\/span><\/code><code><span class=\"code-snippet_outer\">scater::plotPCA(example_sce, colour_by = 'cellTypes', shape = 'batch')<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-indent: 0em;\"><o:page><\/o:page><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014388\" data-ratio=\"0.6175925925925926\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-25_scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01\/16_QibmRbhhyOyuCUVdMAtcGvpZZwya6w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSnNYqXkqcnWE1YkibDx85xgTia2VQibmRbhhyOyuCUVdMAtcGvpZZwya6w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"342.2099914550781\" width=\"553.8099975585938\" \/><\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);\"><strong><span style=\"color: rgb(2, 30, 170);font-size: 15px;\">\u7ed3\u8bed<\/span><\/strong><\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">scMerge2\u80fd\u591f\u5bf9\u5927\u91cf\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u7efc\u5408\u5206\u6790\u3002\u968f\u7740\u516c\u5171\u591a\u6837\u672c\u591a\u6761\u4ef6\u5355\u7ec6\u80de\u7814\u7a76\u7684\u53ef\u7528\u6027\u6301\u7eed\u6fc0\u589e\uff0cscMerge2 \u8bc1\u660e\u4e86\u5176\u6574\u5408\u8d85\u8fc7 500 \u4e07\u4e2a\u7ec6\u80de\u4ee5\u8fdb\u884c\u8fdb\u4e00\u6b65\u4e0b\u6e38\u5206\u6790\u7684\u80fd\u529b\uff0c\u4ece\u800c\u5b9e\u73b0\u6709\u6548\u7684\u4e0b\u6e38\u835f\u8403\u5206\u6790\u3002scMerge2\u5728\u6240\u6709\u4e3b\u8981\u7ec6\u80de\u7c7b\u578b\u7684\u9884\u6d4b\u51c6\u786e\u7387\u65b9\u9762\u6709\u4e86\u663e\u7740\u7684\u63d0\u9ad8\u3002\u6700\u540e\uff0cscMerge2\u80fd\u591f\u7ed3\u5408\u4ece\u5404\u79cd\u5355\u7ec6\u80de\u6280\u672f\uff08\u5982CITE-seq\uff0cCyTOF\u548c\u56fe\u50cf\u8d28\u8c31\u7ec6\u80de\u672f\uff09\u83b7\u5f97\u7684\u6570\u767e\u4e07\u4e2a\u7ec6\u80de\u7684\u6570\u636e\u3002<\/span><span style=\"font-family: \u5b8b\u4f53;font-size: 15px;text-indent: 0em;letter-spacing: 0.034em;\"> <\/span><\/section>\n<section style=\"text-indent: 0em;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u597d\u4e86\uff0c\u5c0f\u679c\u5e26\u7740\u5927\u5bb6\u5df2\u7ecf\u5b66\u4e60\u4e8680%\u7684\u77e5\u8bc6\u4e86\uff0c\u5269\u4e0b\u7684\u5185\u5bb9\u5c31\u4ea4\u7ed9\u5c0f\u4f19\u4f34\u4eec\u4e86\uff01\u6700\u540e\uff0c\u5927\u5bb6\u5982\u679c\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u8fd8\u4e0d\u719f\u6089\uff0c\u53c8\u60f3\u5c1d\u8bd5\u4e00\u4e0b\u5904\u7406\u81ea\u5df1\u7684\u6570\u636e\uff0c\u4e0d\u59a8\u8bd5\u4e00\u4e0b\u5c0f\u679c\u5f00\u53d1\u7684\u751f\u4fe1\u4e91\u5e73\u53f0\u54e6\uff0c\u4e00\u952e\u51fa\u56fe\uff0c\u4e00\u952e\u5bfc\u51faCNS\u7ea7\u522b\u7684Figture\uff01\uff01\u8d76\u5feb\u53bb\u8bd5\u8bd5\u5427\uff01\uff01\u70b9\u51fb <\/span><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;color: rgb(68, 114, 196);\">http:\/\/www.biocloudservice.com\/home.html<\/span><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u3002<\/span><\/span><\/section>\n<section><span style=\"color: rgb(2, 30, 170);\"><strong><span style=\"font-size: 15px;\">\u53c2\u8003\u6587\u732e<\/span><\/strong><\/span><\/section>\n<section><span style=\"font-size: 15px;\">1.scMerge: scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Yingxin Lin, Shila Ghazanfar, Kevin Y.X. Wang, Johann A. Gagnon-Bartsch, Kitty K. Lo, Xianbin Su, Ze-Guang Han, John T. Ormerod, Terence P. Speed, Pengyi Yang, Jean Y. H. Yang. (2019). Our manuscript published at PNAS can be found here.<\/span><\/section>\n<section><span style=\"font-size: 15px;\">2.scMerge2: Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Yingxin Lin, Yue Cao, Elijah Willie, Ellis Patrick, Jean Y.H. Yang. (2023). Our manuscript published in Nature Communications can be found here.  <\/span><\/section>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014389\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/17_VmRkv7tSNKliafDnsuFR7BoeDgBrww.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxPqeNQsFjm2HibIuSld9Nh9GicQSWhJwHjia5tEevQvDIebLErVmRkv7tSNKliafDnsuFR7BoeDgBrww\/640?wx_fmt=jpeg&from=appmsg'\" data-type=\"jpeg\" data-w=\"900\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\" data-recalc-dims=\"1\" \/><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"margin-top: 0pt;margin-bottom: 0pt;margin-left: 0pt;letter-spacing: 0.578px;text-indent: 0pt;text-wrap: wrap;text-align: justify;line-height: normal;font-size: 12pt;font-family: helvetica;color: rgb(0, 0, 0);break-after: auto;\"><span style=\"font-size: 15px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014390\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/18_FbEg9fibwQicL8l2ExKOZZTmAHXabQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAx3HetBkB7aOGibFWKqibqIATyC4zFibzCgdrxFwRep6cDMLIbA0FbEg9fibwQicL8l2ExKOZZTmAHXabQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;caret-color: rgba(0, 0, 0, 0);\" 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