{"id":29412,"date":"2024-02-22T17:58:36","date_gmt":"2024-02-22T09:58:36","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29412"},"modified":"2024-02-22T17:58:38","modified_gmt":"2024-02-22T09:58:38","slug":"%e5%8d%95%e7%bb%86%e8%83%9e%e4%b8%8d%e5%90%8c%e7%b1%bb%e5%9e%8b%e6%b5%8b%e5%ba%8f%e6%96%87%e4%bb%b6%e8%af%bb%e5%8f%96","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29412","title":{"rendered":"\u5355\u7ec6\u80de\u4e0d\u540c\u7c7b\u578b\u6d4b\u5e8f\u6587\u4ef6\u8bfb\u53d6"},"content":{"rendered":"

\u5355\u7ec6\u80de\u4e0d\u540c\u7c7b\u578b\u6d4b\u5e8f\u6587\u4ef6\u8bfb\u53d6<\/p>\n

\u5728\u8fdb\u884c\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u65f6\uff0c\u7b2c\u4e00\u6b65\u5c31\u662f\u5355\u7ec6\u80de\u6d4b\u5e8f\u6587\u4ef6\u7684\u8bfb\u5165\uff0c\u5355\u7ec6\u80de\u6587\u4ef6\u5f62\u5f0f\u5404\u79cd\u5404\u6837\uff0c<\/p>\n

\u4eca\u5929\u5c0f\u679c\u8bb2\u89e3\u4e00\u4e0b\u51e0\u79cd\u4e0d\u540c\u7c7b\u578b\u6587\u4ef6\u7684\u8bfb\u5165\u65b9\u6cd5\uff0c\u65b9\u6cd5\u5982\u4e0b\uff1a<\/p>\n

1.10X\u7684\u5355\u7ec6\u80de\u6587\u4ef6<\/p>\n

#\u8bfb\u53d6\u6570\u636e10X\u6570\u636e\u6240\u5728\u7684\u6587\u4ef6\u5939<\/p>\n

pbmc.data <- Read10X(data.dir = “filtered_gene_bc_matrices\/hg19\/”)<\/p>\n

\"Dingtalk_20230308103719\"<\/p>\n

#\u521b\u5efaSeurat\u6587\u4ef6<\/p>\n

pbmc <- CreateSeuratObject(counts = pbmc.data, project = “pbmc3k”, min.cells = 3, min.features = 200)<\/p>\n

    \n
  1. \u8f93\u5165\u6570\u636e\u662f\u57fa\u4e8eUMI\u7684\u8868\u8fbe\u77e9\u9635(\u5176\u4e2d\u6570\u636e\u96c6\u4e2d\u7684\u884c\u8868\u793a\u57fa\u56e0\uff0c\u5217\u8868\u793a\u7ec6\u80de)<\/li>\n<\/ol>\n

    molecules <- read.delim(“molecules.txt”,header = TRUE,<\/p>\n

    row.names = 1)<\/p>\n

    \"Dingtalk_20230308151643\"<\/p>\n

    #\u521b\u5efaSeurat\u6587\u4ef6<\/p>\n

    obj <- CreateSeuratObject(counts = molecules,<\/p>\n

    min.cells = 3, #\u7b5b\u9009\u81f3\u5c11\u57283\u4e2a\u7ec6\u80de\u4e2d\u8868\u8fbe\u7684\u57fa\u56e0<\/p>\n

    min.features = 200) #\u7b5b\u9009\u81f3\u5c11\u6709200\u4e2a\u57fa\u56e0\u8868\u8fbe\u7684\u7ec6\u80de<\/p>\n

    #\u589e\u52a0Seurat\u7684\u5143\u4fe1\u606f(metadata)<\/p>\n

    ann <- read.delim(“annotation.txt”, header = TRUE)<\/p>\n

    \"Dingtalk_20230308151751\"<\/p>\n

    rownames(ann) <- ann$sample_id<\/p>\n

    obj <- AddMetaData(obj, ann)<\/p>\n

      \n
    1. \u8f93\u5165\u6570\u636e\u662fh5\u6587\u4ef6\u683c\u5f0f<\/li>\n<\/ol>\n

      devtools::install_github(repo = “hhoeflin\/hdf5r”)<\/p>\n

      library(hdf5r)<\/p>\n

      obj<-Read10X_h5(“GSE154989_mmLungPlate_fQC_dSp_rawCount.h5”)<\/p>\n

      obj <- CreateSeuratObject(counts = obi, project=\u201dobj\u201d,<\/p>\n

      min.cells = 3, #\u7b5b\u9009\u81f3\u5c11\u57283\u4e2a\u7ec6\u80de\u4e2d\u8868\u8fbe\u7684\u57fa\u56e0<\/p>\n

      min.features = 200) #\u7b5b\u9009\u81f3\u5c11\u6709200\u4e2a\u57fa\u56e0\u8868\u8fbe\u7684\u7ec6\u80de<\/p>\n

        \n
      1. \u5229\u7528SeuratData\u5305\u5bfc\u5165\u5185\u7f6e\u6570\u636e<\/strong><\/li>\n<\/ol>\n

        devtools::install_github(‘satijalab\/seurat-data’,force = TRUE)<\/strong><\/p>\n

        library(SeuratData)<\/strong><\/p>\n

        InstallData(“ifnb”)<\/strong><\/p>\n

        LoadData(“ifnb”)<\/strong><\/p>\n

          \n
        1. Seurat\u5bf9\u8c61<\/li>\n<\/ol>\n

          \u5982\u679c\u6587\u4ef6\u662f\u5df2\u7ecf\u6784\u5efa\u597d\u7684seurat\u5bf9\u8c61\uff0c\u540e\u671f\u53ef\u4ee5\u76f4\u63a5\u8fdb\u884c\u8d28\u63a7\u548c\u5355\u7ec6\u80de\u5206\u6790\u6d41\u7a0b\uff1b\u5982\u679c\u53d1\u73b0\u53d1\u73b0\u4e0a\u4f20seurat\u7248\u672c\u8f83\u4f4e\uff0c\u9700\u8981\u66f4\u65b0\u8f6c\u5316\u3002<\/p>\n

          obj<-UpdataSeuratObject(object=obj)<\/p>\n

          \u5355\u7ec6\u80de\u6d4b\u5e8f\u6587\u4ef6\u7c7b\u578b\u5927\u6982\u5c31\u8fd9\u51e0\u79cd\uff0c\u5728\u8fdb\u884c\u6570\u636e\u8bfb\u5165\u65f6\u53ef\u4ee5\u6309\u7167\u6570\u636e\u7c7b\u578b\u9009\u62e9\u4e0d\u540c\u7684\u65b9\u6cd5\u8fdb\u884c\u8bfb\u53d6\uff0c\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u70b9\u8d5e\u6536\u85cf\u52a0\u4e2a\u5173\u6ce8\u5965\uff0c\u4e0b\u671f\u518d\u89c1\u5965\uff01\uff01\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"

          \u5355\u7ec6\u80de\u4e0d\u540c\u7c7b\u578b\u6d4b\u5e8f\u6587\u4ef6\u8bfb\u53d6 \u5728\u8fdb\u884c\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u65f6\uff0c\u7b2c\u4e00\u6b65\u5c31\u662f\u5355\u7ec6\u80de\u6d4b\u5e8f\u6587\u4ef6\u7684\u8bfb\u5165\uff0c\u5355\u7ec6\u80de\u6587\u4ef6\u5f62\u5f0f\u5404\u79cd\u5404\u6837\uff0c […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29412"}],"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=29412"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29412\/revisions"}],"predecessor-version":[{"id":29418,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29412\/revisions\/29418"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29412"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29412"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29412"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}