{"id":25613,"date":"2024-01-22T17:16:28","date_gmt":"2024-01-22T09:16:28","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25613"},"modified":"2024-01-22T17:16:29","modified_gmt":"2024-01-22T09:16:29","slug":"%e8%b6%85%e7%ba%a7%e8%b6%85%e7%ba%a7%e7%89%9b%e7%9a%84iobr%e5%8c%85%ef%bc%8c%e4%b8%80%e5%8c%85%e8%a7%a3%e5%86%b37%e7%a7%8d%e5%85%8d%e7%96%ab%e6%b5%b8%e6%b6%a6%e5%88%86%e6%9e%90%e6%96%b9%e6%b3%95","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25613","title":{"rendered":"\u8d85\u7ea7\u8d85\u7ea7\u725b\u7684IOBR\u5305\uff0c\u4e00\u5305\u89e3\u51b37\u79cd\u514d\u75ab\u6d78\u6da6\u5206\u6790\u65b9\u6cd5"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u4e3a\u5927\u5bb6\u5e26\u6765\u7684\u5206\u4eab\u7070\u5e38\u7070\u5e38\u6709\u7528\uff0c\u5bf9\u4e8e\u5f88\u591a\u5c0f\u4f19\u4f34\u6765\u8bf4\uff0c\u514d\u75ab\u6d78\u6da6\u5206\u6790\u662f\u975e\u5e38\u719f\u6089\u7684\u5206\u6790\u5185\u5bb9\uff0c\u514d\u75ab\u6d78\u6da6\u5206\u6790\u65b9\u6cd5\u4e3b\u8981\u5305\u62ecxcell,MCP-counter,timer,quantiseq\uff0cepic\uff0ccibersort\uff0cestimate\u7b49\u65b9\u6cd5\uff0c\u4f46\u662f\u8fd9\u51e0\u79cd\u65b9\u6cd5\u90fd\u6709\u5404\u81ea\u7684R\u5305\u6765\u8fdb\u884c\u5206\u6790\uff0c\u6709\u51e0\u79cd\u65b9\u6cd5\u5c31\u9700\u8981\u5b89\u88c5\u548c\u5b66\u4e60\u51e0\u79cdR\u5305\uff0c\u5bf9\u5c0f\u767d\u548c\u521d\u5b66\u8005\u6765\u8bf4\u975e\u5e38\u4e0d\u53cb\u597d\uff0c\u9700\u8981\u82b1\u8d39\u5927\u91cf\u7684\u65f6\u95f4\uff0c\u57fa\u4e8e\u8fd9\u79cd\u60c5\u51b5\uff0c\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u63a8\u8350\u4e00\u4e2aR\u5305IOBR\uff0c\u8be5\u5305\u76f4\u63a5\u53ef\u4ee5\u5b8c\u6210\u591a\u79cd\u7b97\u6cd5\u7684\u514d\u75ab\u6d78\u6da6\u5206\u6790\uff0c\u6bcf\u4e2a\u7b97\u6cd5\u90fd\u53ea\u9700\u8981\u4e00\u53e5\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u7b80\u5355\u5965\uff01\u5c0f\u679c\u5f3a\u70c8\u63a8\u8350\uff0c\u63a5\u4e0b\u6765\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\u5b66\u4e60\u3002<\/p>\n

    \n
  1. \u5b89\u88c5IOBR\u5305<\/li>\n<\/ol>\n

    \u9996\u5148\u5c0f\u679c\u4e3a\u5927\u5bb6\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b\u5982\u4f55\u5b89\u88c5\u548c\u5b66\u4e60IOBR\u5305\uff0c\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u4eec\u9644\u4e0a\u7f51\u5740\uff1ahttps:\/\/iobr.github.io\/IOBR\/IOBR-VIGNETTE.html\uff0c\u60f3\u6df1\u5165\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u5230\u8be5\u7f51\u5740\u5b66\u4e60\u3002<\/p>\n

    \"Dingtalk_20230716172700\"<\/p>\n

    #\u9700\u8981\u6ce8\u610f\u7684\u662f\u5b98\u7f51\u63a8\u8350\u4f7f\u7528github\u7684\u65b9\u6cd5\u6765\u5b89\u88c5\uff0c\u4f46\u662f\u7531\u4e8e\u7f51\u7edc\u95ee\u9898\uff0c\u901a\u8fc7github\u5b89\u88c5\u975e\u5e38\u975e\u5e38\u6162\uff0c\u4e00\u822c\u90fd\u4e0d\u80fd\u5b89\u88c5\u6210\u529f\uff0c\u56e0\u6b64\u5c0f\u679c\u63a8\u8350\u76f4\u63a5\u4e0b\u8f7d\u5b89\u88c5\u5305\uff0c\u8fdb\u884c\u672c\u5730\u5b89\u88c5\uff0c\u5b89\u88c5\u901f\u5ea6\u975e\u5e38\u5feb\uff01\u5b89\u88c5\u5305\u53ef\u4ee5\u5230\u8be5\u7f51\u5740\u4e0b\u8f7d\uff1ahttps:\/\/github.com\/IOBR\/IOBR\u3002<\/p>\n

    #\u9996\u5148\u5b89\u88c5\u4f9d\u8d56\u7684R\u5305<\/p>\n

    if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”)<\/p>\n

    depens<-c(‘tibble’, ‘survival’, ‘survminer’, ‘sva’, ‘limma’, “DESeq2″,”devtools”,<\/p>\n

    ‘limSolve’, ‘GSVA’, ‘e1071’, ‘preprocessCore’, ‘ggplot2’, “biomaRt”,<\/p>\n

    ‘ggpubr’, “devtools”, “tidyHeatmap”, “caret”, “glmnet”, “ppcor”, “timeROC”,”pracma”)<\/p>\n

    for(i in 1:length(depens)){<\/p>\n

    depen<-depens[i]<\/p>\n

    if (!requireNamespace(depen, quietly = TRUE))<\/p>\n

    BiocManager::install(depen,update = FALSE)<\/p>\n

    }<\/p>\n

    #\u5b89\u88c5IOBR\u5305<\/p>\n

    install.packages(“IOBR-master.tar.gz”,repos=NULL,type=”source”)<\/p>\n

    #\u52a0\u8f7dIOBR\u5305<\/p>\n

    library(IOBR)<\/p>\n

      \n
    1. \u51e0\u79cd\u514d\u75ab\u7b97\u6cd5\u7684\u7b80\u5355\u4ecb\u7ecd<\/li>\n<\/ol>\n

      #quanTIseq\u7b97\u6cd5\u7b80\u5355\u4ecb\u7ecd<\/p>\n

      quanTIseq\u662f\u7528\u4e8e\u6839\u636e\u4eba\u7c7bRNA-seq\u6570\u636e\u91cf\u5316\u80bf\u7624\u514d\u75ab\u72b6\u51b5\uff0c\u901a\u8fc7\u53cd\u5377\u79ef\u91cf\u5316\u6837\u672c\u4e2d\u5b58\u5728\u768410\u79cd\u4e0d\u540c\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u6bd4\u4f8b\u4ee5\u53ca\u5176\u4ed6\u672a\u8868\u5f81\u7ec6\u80de\u7684\u6bd4\u4f8b\u3002<\/p>\n

      #xcell\u7b97\u6cd5\u7b80\u5355\u4ecb\u7ecd<\/p>\n

      xcell\u662f\u57fa\u4e8essGSEA\u7684\u65b9\u6cd5\uff0c\u53ef\u6839\u636e64\u79cd\u514d\u75ab\u7ec6\u80de\u548c\u57fa\u8d28\u7ec6\u80de\u7c7b\u578b\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u7ec6\u80de\u7c7b\u578b\u5bcc\u96c6\u5206\u6790\u3002<\/p>\n

      #TIMER\u7b97\u6cd5\u7b80\u5355\u4ecb\u7ecd<\/p>\n

      TIMER\u7528\u53cd\u5377\u79ef\u65b9\u6cd5\u4f30\u7b9732\u79cd\u764c\u75c7\u4e2d\u516d\u79cd\u514d\u75ab\u7ec6\u80de\u4e30\u5ea6\uff0c\u9700\u8981\u6ce8\u610f\u7684\u662fTIMER\u6709\u5728\u7ebf\u7684\u7f51\u7ad9\u53ef\u4ee5\u76f4\u63a5\u8fdb\u884c\u5206\u6790\u3002<\/p>\n

      #EPIC\u7b97\u6cd5\u7b80\u5355\u4ecb\u7ecd<\/p>\n

      EPIC\u4f7f\u7528\u7ea6\u675f\u6700\u5c0f\u4e8c\u4e58\u56de\u5f52\u5c06\u8d1f\u6027\u7ea6\u675f\u6761\u4ef6\u7eb3\u5165\u53cd\u5377\u79ef\u95ee\u9898\uff0c\u4ece\u5927\u91cf\u80bf\u7624\u6837\u672c\u7684\u8868\u8fbe\u8c31\u6570\u636e\u8fdb\u884c\u5206\u6790\u3002<\/p>\n

      3.\u8bfb\u53d6\u8f93\u5165\u6570\u636e<\/p>\n

      #EXP.txt\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff0c\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u5217\u540d\u4e3a\u6837\u672c\u540d<\/p>\n

      dat <- read.table(“EXP.txt”,sep = “\\t”,row.names = 1,header = T,stringsAsFactors = F,check.names = F)<\/p>\n

      \"Dingtalk_20230716172956\"<\/p>\n

        \n
      1. \u901a\u8fc7IOBR\u5305\u91c7\u7528\u591a\u79cd\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/li>\n<\/ol>\n

        #\u5229\u7528CIBERSORT\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/p>\n

        cibersort<-deconvo_tme(eset = dat, method = “cibersort”, arrays = FALSE, perm = 200 )<\/p>\n

        \"Dingtalk_20230716150931\"<\/p>\n

        #\u5229\u7528EPIC\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/p>\n

        epic<-deconvo_tme(eset = dat, method = “epic”, arrays = FALSE)<\/p>\n

        \"Dingtalk_20230716151515\"<\/p>\n

        #\u5229\u7528mcpcounter\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/p>\n

        mcp<-deconvo_tme(eset = dat, method = “mcpcounter”)<\/p>\n

        \"Dingtalk_20230716151825\"<\/p>\n

        #\u5229\u7528xCELL\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/p>\n

        xcell<-deconvo_tme(eset = dat, method = “xcell”,arrays = FALSE)<\/p>\n

        \"Dingtalk_20230716152125\"<\/p>\n

        #\u5229\u7528estimate\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/p>\n

        estimate<-deconvo_tme(eset = dat, method = “estimate”)<\/p>\n

        \"Dingtalk_20230716152617\"<\/p>\n

        #\u5229\u7528TIMER\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/p>\n

        timer<-deconvo_tme(eset = dat, method = “timer”, group_list = rep(“stad”,dim(dat)[2]))<\/p>\n

        \"Dingtalk_20230716153100\" #\u5229\u7528quanTIseq\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/p>\n

        quantiseq<-deconvo_tme(eset = dat, tumor = TRUE, arrays = FALSE, scale_mrna = TRUE, method = “quantiseq”)<\/p>\n

        \"Dingtalk_20230716153657\"<\/p>\n

        #\u8fde\u63a57\u79cd\u7b97\u6cd5\u514d\u75ab\u5206\u6790\u7ed3\u679c<\/p>\n

        tme_combine<-cibersort %>%<\/p>\n

        inner_join(.,mcp,by = “ID”) %>%<\/p>\n

        inner_join(.,xcell,by = “ID”) %>%<\/p>\n

        inner_join(.,epic,by = “ID”) %>%<\/p>\n

        inner_join(.,estimate,by = “ID”) %>%<\/p>\n

        inner_join(.,timer,by = “ID”) %>%<\/p>\n

        inner_join(.,quantiseq,by = “ID”)<\/p>\n

        \"Dingtalk_20230716180932\"<\/p>\n

        #IPS\u514d\u75ab\u8868\u578b\u8bc4\u5206\u8ba1\u7b97<\/p>\n

        ips<-deconvo_tme(eset = dat, method = “ips”, plot= FALSE)<\/p>\n

        \"Dingtalk_20230717141334\"<\/p>\n

        \u6700\u7ec8\u5c0f\u679c\u6210\u529f\u7684\u5229\u7528IOBR\u5305\u7b97\u6cd5\u8fdb\u884c\u4e86\u514d\u75ab\u6d78\u6da6\u5206\u6790\uff0c\u5305\u62ecCIBERSORT\uff0cEPIC\uff0cmcpcounter\uff0cxCELL\uff0cestimate\uff0cTIMER\uff0cquanTIseq 7\u79cd\u7b97\u6cd5,\u6700\u540e\u8fd8\u8ba1\u7b97\u4e86\u514d\u75ab\u8868\u578b\u8bc4\u5206(IPS),\u8be5\u5305\u5206\u6790\u6548\u679c\u975e\u5e38\u4e0d\u9519\uff0c\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u5440\uff01\u514d\u75ab\u6d78\u6da6\u76f8\u5173\u5206\u6790\u5185\u5bb9\uff0c\u4f8b\u5982\u5355\u6837\u672c\u5bcc\u96c6\u7b97\u6cd5\u5206\u6790\u514d\u75ab\u6d78\u6da6\u4e30\u5ea6(http:\/\/www.biocloudservice.com\/106\/106.php)\uff0c\u8ba1\u7b9764\u79cd\u514d\u75ab\u7ec6\u80de\u76f8\u5bf9\u542b\u91cf(http:\/\/www.biocloudservice.com\/107\/107.php)\uff0cpanImmune\u514d\u75ab\u6d78\u6da6\u5206\u6790(http:\/\/www.biocloudservice.com\/782\/782.php)\uff0c\u57fa\u4e8e\u57fa\u56e0\u8868\u8fbe\u8c31\u4f30\u7b97\u6837\u672c\u514d\u75ab\u57fa\u8d28\u8bc4\u5206\u548c\u80bf\u7624\u7eaf\u5ea6(http:\/\/www.biocloudservice.com\/114\/114.php)\u7b49\u90fd\u53ef\u4ee5\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u5e73\u53f0\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u4e00\u952e\u5b8c\u6210\u8be5\u5206\u6790\u5965\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u5c1d\u8bd5\u5965\uff0c\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u4e0b\u671f\u5728\u89c1\u5965\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5c0f\u679c\u4e3a\u5927\u5bb6\u5e26\u6765\u7684\u5206\u4eab\u7070\u5e38\u7070\u5e38\u6709\u7528\uff0c\u5bf9\u4e8e\u5f88\u591a\u5c0f\u4f19\u4f34\u6765\u8bf4\uff0c\u514d\u75ab\u6d78\u6da6\u5206\u6790\u662f\u975e\u5e38\u719f\u6089\u7684\u5206\u6790\u5185\u5bb9\uff0c\u514d\u75ab\u6d78\u6da6\u5206\u6790\u65b9\u6cd5\u4e3b […]<\/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\/25613"}],"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=25613"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25613\/revisions"}],"predecessor-version":[{"id":25627,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25613\/revisions\/25627"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25613"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25613"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25613"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}