{"id":58633,"date":"2024-06-16T23:19:25","date_gmt":"2024-06-16T15:19:25","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=58633"},"modified":"2026-09-11T23:07:49","modified_gmt":"2026-09-11T15:07:49","slug":"%e5%b0%8f%e6%9e%9c%e7%9a%84%e5%8d%95%e7%bb%86%e8%83%9e%e5%88%86%e6%9e%90%e4%bf%9d%e5%a7%86%e7%ba%a7%e6%95%99%e7%a8%8b%ef%bc%81%e6%89%8b%e6%8a%8a%e6%89%8b%e6%95%99%e4%bd%a0%e4%bb%8e%e5%8d%95%e7%bb%86","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/%e5%b0%8f%e6%9e%9c%e7%9a%84%e5%8d%95%e7%bb%86%e8%83%9e%e5%88%86%e6%9e%90%e4%bf%9d%e5%a7%86%e7%ba%a7%e6%95%99%e7%a8%8b%ef%bc%81%e6%89%8b%e6%8a%8a%e6%89%8b%e6%95%99%e4%bd%a0%e4%bb%8e%e5%8d%95%e7%bb%86\/","title":{"rendered":"\u5c0f\u679c\u7684\u5355\u7ec6\u80de\u5206\u6790\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\u624b\u628a\u624b\u6559\u4f60\u4ece\u5355\u7ec6\u80de\u6570\u636e\u4e0b\u8f7d\u548c\u5904\u7406\u5230\u5355\u7ec6\u80de\u6ce8\u91ca\uff01\uff01"},"content":{"rendered":"<aside class=\"ysx-source-note\"><span>\u6765\u6e90<\/span><\/p>\n<p>\u516c\u4f17\u53f7\u300c\u751f\u4fe1\u56fe\u300d\u5386\u53f2\u5185\u5bb9\uff1b\u672c\u6587\u4fdd\u7559\u539f\u6709\u6280\u672f\u4fe1\u606f\u5e76\u4f18\u5316\u7f51\u9875\u6392\u7248\u3002 <a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=MzkxODUxNDgzNA==&amp;mid=2247487257&amp;idx=1&amp;sn=b2b6ff08473e3b13c54b8459d880d248\" target=\"_blank\" rel=\"noopener noreferrer nofollow\">\u67e5\u770b\u539f\u6587<\/a><\/p>\n<\/aside>\n<p>\u6700\u8fd1\u5355\u7ec6\u80de\u7684\u6570\u636e\u5206\u6790\u53c8\u6084\u6084\u7684\u706b\u4e86\u8d77\u6765\uff0c\u5c0f\u4f19\u4f34\u4e5f\u4e86\u89e3\u4e86\u4e0d\u5c11\uff0c\u4f46\u662f\u4e0d\u77e5\u9053\u4ece\u4f55\u4e0b\u624b\uff0c\u800c\u4e14\u5462\u6709\u5173\u5355\u7ec6\u80de\u6570\u636e\u7684\u4e0b\u8f7d\u4e5f\u662f\u4e00\u5934\u96fe\u6c34\u3002\u5176\u5b9e\u5462\u5355\u7ec6\u80de\u6570\u636e\u5904\u7406\u4e5f\u5e76\u4e0d\u662f\u5f88\u590d\u6742\uff0c\u53ea\u662f\u5165\u95e8\u4e0d\u5bb9\u6613\uff0c\u4e00\u65e6\u4e0a\u624b\u540e\u7eed\u7684\u5206\u6790\u5c31\u5f88\u7b80\u5355\u3002\u8fd8\u6709\u5462\uff0c\u6211\u4eec\u5728\u505a\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\u5206\u6790\u65f6\u5019\uff0c\u4ed6\u7684\u96be\u70b9\u4e3b\u8981\u5728\u4e8e\u7ec6\u80de\u7684\u8d28\u91cf\u4e0d\u786e\u5b9a\uff0c\u7ec6\u80de\u7684\u6570\u91cf\u5927\uff0c\u4ece\u5355\u7ec6\u80de\u6d4b\u5e8f\u6280\u672f\u8bde\u751f\u81f3\u4eca\uff0c\u6d4b\u5230\u7684\u7ec6\u80de\u901a\u91cf\u8d8a\u6765\u8d8a\u9ad8\u3002\u6240\u4ee5\u5c0f\u679c\u8fd9\u91cc\u51fa\u4e00\u671f\u6559\u7a0b\u53ef\u4ee5\u6559\u5c0f\u4f19\u4f34\u5165\u95e8\u5355\u7ec6\u80de\uff0c\u8ba9\u6211\u4eec\u4ece\u6570\u636e\u4e0b\u8f7d\u5230\u5904\u7406\uff0c\u5c0f\u4f19\u4f34\u5b66\u4f1a\u4e86\u4e4b\u540e\uff0c\u53ef\u4ee5\u4e86\u89e3\u5355\u7ec6\u80de\u5904\u7406\u7684\u5927\u81f4\u6d41\u7a0b\u3002\u4e0b\u9762\u5c0f\u679c\u5462\uff0c\u5c31\u5e26\u5c0f\u4f19\u4f34\u53bb\u4e0b\u8f7d\u81ea\u5df1\u9700\u8981\u7684\u5355\u7ec6\u80de\u6570\u636e\u8fd8\u6709\u5982\u4f55\u53bb\u5904\u7406\u3002<\/p>\n<h2>\u4ece GEO \u83b7\u53d6\u5355\u7ec6\u80de\u6570\u636e<\/h2>\n<p>\u6211\u4eec\u4e00\u822c\u7684\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u5904\u7406\u5462\uff0c\u80af\u5b9a\u662f\u9700\u8981\u548c\u81ea\u5df1\u505a\u7684\u75be\u75c5\u6216\u8005\u80bf\u7624\u76f8\u5173\u7684\u5355\u7ec6\u80de\u6570\u636e\u96c6\uff0c\u6211\u4eec\u5f80\u5f80\u7528\u7684\u505a\u7684\u4e0b\u8f7d\u65b9\u5f0f\u5c31\u662f\u5728NCBI\u8fd9\u4e2a\u5e73\u53f0\uff0cGEO\u6570\u636e\u5e93\u6536\u96c6\uff0c\u4e0b\u9762\u5c0f\u679c\u5c31\u5e26\u5c0f\u4f19\u4f34\u770b\u770b\u5982\u4f55\u53bb\u4e0b\u8f7d\uff01<\/p>\n<p>\u6211\u4eec\u4e00\u822c\u6253\u5f00\u8fd9\u4e2a\u7f51\u5740\uff1ahttps:\/\/www.ncbi.nlm.nih.gov\/<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_MT3apibaLcULmicticv7I56yHtsywQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u5728\u8fd9\u91cc\u8f93\u5165\u6211\u4eec\u7684\u76f8\u5173\u7684\u4fe1\u606f\u641c\u7d22\uff0c\u8fd9\u91cc\u5c0f\u56fe\u8bd5\u9a8c\u80ba\u764c\u8fdb\u884c\u5c55\u793a\uff0clung cancer \u6211\u4eec\u5728\u641c\u7d22\u7684\u65f6\u5019\u540e\u9762\u8981\u52a0\u5165\u5355\u7ec6\u80de\u76f8\u5173\u7684\u5173\u952e\u5b57\uff0clung caner scRNAseq \u7136\u540e\u5728\u52a0\u4e0a human\u4eba\u7c7b\uff0c\u4e00\u822c\u5c31\u4f7f\u7528lung caner scRNAseq human \u5982\u679c\u662f\u5176\u4ed6\u75be\u75c5 \u6362\u4e00\u4e0b\u5c31\u53ef\u4ee5\uff0c\u6bd4\u5982\u5bab\u9888\u764c cervical cancer scRNAseq human<\/p>\n<p>\u6765\u770b\u770b\u6548\u679c  \u00a0 \u00a0<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ibDc1EOSibeicT3VFrnyAdTFbvgtIA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u91cc\u9700\u8981\u628a\u641c\u7d22\u6765\u6e90\u9009\u62e9GEO\u6570\u636e\u5e93\uff0c\u7136\u540e\uff1a<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_s95u7sic8kFdmbibOq25v7U7nIwEyQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u7136\u540e\u5c31\u4f1a\u6709\u4e0b\u9762\u7684\u754c\u9762\uff0c\u8fd9\u5c31\u9700\u8981\u5c0f\u4f19\u4f34\u53bb\u81ea\u884c\u53bb\u9009\u62e9\uff0c\u6211\u4eec\u968f\u673a\u70b9\u51fb\u67e5\u770b\u4e00\u4e0b<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_ug8Jg3OJiccEGsA1YPutFZdXj64H5Q.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_kIUzNPwwL7uXnZoNmP9pV4RGZ0pb6g.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"> \u00a0 \u00a0<\/p>\n<p>\u8fd9\u91cc\u6709\u5f88\u591a\u5355\u7ec6\u80de\u6570\u636e\uff0c\u5176\u5b9e\u6211\u4eec\u9009\u62e9\u4e0b\u8f7d\u7684\u4e5f\u662f\u6709\u76ee\u7684\u7684\uff0c\u6211\u4eec\u5982\u679c\u9009\u62e9<img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_OjRIcJV0tZdIwxibcKes5ERjsVHHKw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u4e09\u4e2a\u91cc\u9762\u7684\u4e00\u79cd\uff0c\u70b9\u51fb\u8fdb\u53bb\u4e0b\u8f7d<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_NIjtQib3eiayYpsVlDeMWadS9FsZJA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_yopfkHSGV16twFXABnRicboVmqtESQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u4e0b\u8f7d\u8fd9\u4e2a\u5c31\u53ef\u4ee5\uff0c\u8fd9\u79cd\u662fCSV\u683c\u5f0f\u7684\uff0c\u4e0b\u9762\u5c0f\u679c\u4f1a\u6559\u5c0f\u4f19\u4f34\u5bfc\u5165\u6570\u636e\u683c\u5f0f\u7684\u65b9\u5f0f\uff0c\u5176\u5b9e\u6211\u4eec\u4e0b\u8f7d\u6570\u636e\u96c6\u53ef\u80fd\u8fd8\u6709\u5176\u4ed6\u6570\u636e\u683c\u5f0f\uff0c\u4e00\u822c\u6700\u591a\u7684\u5c31\u662fH5\u683c\u5f0f\uff0c\u8fd8\u6709mtx\u683c\u5f0f\uff0c\u8fd9\u91cc\u5c0f\u4f19\u4f34\u4e0d\u7528\u62c5\u5fc3\uff0c\u5c0f\u679c\u90fd\u4f1a\u6559\u5c0f\u4f19\u4f34\uff0c\u6211\u4eec\u6765\u770b\u4e00\u4e2aH5\u683c\u5f0f\u7684\uff0c<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_UL11RDbvn9E5Bje6kBkzycHQ3iamfA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u4e0b\u8f7d\u8fd8\u89e3\u538b\u540e<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_aD54fiaERkTXRBWXozbgSPfh3Tu5hg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u5c31\u4f1a\u8fd9\u6837\uff0c \u00a0 \u00a0<\/p>\n<p>\u8fd8\u6709\u4e00\u79cd<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_RnE1o8KZemsQiaIzqsOficmPickGCQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<h2>\u5bfc\u5165 H5\u3001MTX \u548c CSV \u6570\u636e<\/h2>\n<p>\u6211\u4eec\u5148\u4eceH5\u683c\u5f0f\u5b66\u4e60\uff0c\u8fd9\u4e2a\u6bd4\u8f83\u7b80\u5355\u4e00\u884c\u4ee3\u7801\u5c31\u5b66\u4f1a\u4e86\uff0c\u8fd9\u91cc\u5c0f\u679c\u968f\u4fbf\u7528\u4e00\u4e2a\u6570\u636e\u96c6\u5c55\u793a\uff0c<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>library(hdf5r)<\/code><code>library(Seurat)<\/code><code>library(dplyr)<\/code><\/pre>\n<\/div>\n<p>\u6211\u4eec\u8fd8\u8981\u52a0\u8f7d\u4e00\u4e0b\u8fd9\u4e2a\u5305\uff0c\u7528\u6765\u5904\u7406\u6570\u636e\u7684<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>data_sample &lt;- Read10X_h5(\"GSM4983457_NC_filtered_feature_bc_matrix.h5\")  #\u5bfc\u5165H5\u683c\u5f0f\u6570\u636e<\/code><code>data_seurat &lt;- CreateSeuratObject(data_sample,project = \"data_sample\") #\u540e\u9762\u5c31\u53ef\u4ee5\u8fdb\u884c\u5355\u7ec6\u80de\u5904\u7406\u7684\u6807\u51c6\u6d41\u7a0b\u4e86<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_fSDeCAWiamf8z29Z8UvMXnR9brNACA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u6837\u5c31\u5bfc\u5165\u6210\u529f\u4e86\uff0c<\/p>\n<p>\u4e0b\u9762\u6211\u4eec\u5bf9mtx\u683c\u5f0f\u8fdb\u884c\u5bfc\u5165\uff0c<\/p>\n<p>\u800c\u6211\u4eec\u5f80\u5f80\u4e0b\u8f7dmtx\u683c\u5f0f\u7684\u4e00\u822c\u4f1a\u6709\u8fd9\u4e09\u4e2a\u6587\u4ef6<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/13_VAaWXUDHCeCBHpYZfCSGiaqCVWvpxA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code># \u8bfb\u53d610x\u6570\u636e\uff0cdata.dir\u53c2\u6570\u6307\u5b9a\u5b58\u653e\u6587\u4ef6\u7684\u8def\u5f84    <\/code><code>seurat_data &lt;- Read10X(data.dir = \"E:\\JYStudio\\Rtest\\Ztest1\\\u5355\u7ec6\u80de\\\u5355\u7ec6\u80de\u6570\u636e\u5904\u7406\\Tumor\")<\/code><code>##\u8fd9\u4e2a\u5c0f\u4f19\u4f34\u8981\u81ea\u884c\u8bbe\u7f6e\u5b58\u653e\u8fd9\u4e2a\u6587\u4ef6\u7684\u76ee\u5f55\uff0c<\/code><code># \u7136\u540e\u6211\u4eec\u521b\u5efaSeurat\u5bf9\u8c61<\/code><code>data_seurat &lt;- CreateSeuratObject(counts = seurat_data,<\/code><code>                                 project = \"GSM5155196_352\",<\/code><code>                                 min.features = 200,<\/code><code>                                 min.cells = 3)<\/code><code>\u8fd9\u4e2a\u5c31\u548c\u4e0a\u8ff0\u521b\u5efa\u5bf9\u8c61\uff0c\u540e\u7eed\u5c31\u53ef\u4ee5\u8fdb\u884c\u5355\u7ec6\u80de\u7684\u6807\u51c6\u6d41\u7a0b\u4e86<\/code><code>\u4f7f\u7528\u8fd9\u4e2a\u4ee3\u7801\u5c31\u53ef\u4ee5\u5bfc\u5165\u6570\u636e\uff0c<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/14_W9zyn1LMljVCx9Qy2prclk3iaxF8Ww.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u5bfc\u5165\u540e\u5c31\u662f\u4e00\u6837\u7684\uff0c<\/p>\n<p>\u6700\u540e\u4e00\u79cd\u5c31\u662fcsv\u683c\u5f0f\u7684\uff0c\u5c0f\u4f19\u4f34\u6709\u7684\u4e0b\u8f7d\u53ea\u6709csv\u683c\u5f0f\u7684\u600e\u4e48\u529e\uff0c\u5c0f\u679c\u8fd9\u91cc\u6559\u5927\u5bb6<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>##\u7b2c\u4e8c\u79cd<\/code><code>library(tidyr)<\/code><code>library(tidyverse)<\/code><code>library(org.Mm.eg.db)<\/code><code>library(scater)<\/code><code>library(scran)<\/code><code>library(pheatmap)<\/code><code>library(limma)    <\/code><code>library(edgeR)<\/code><code>library(dynamicTreeCut)<\/code><code>library(cluster)<\/code><code>library(monocle)<\/code><code>aa &lt;- read.csv(\"GSE122340.csv\",row.names = 1,header = T)<\/code><code>all.counts &lt;- as.matrix(aa)<\/code><code>pbmc &lt;- CreateSeuratObject(counts = all.counts, project = \"TCGA\", names.delim = \"-\",<\/code><code>                           min.cells = 3, min.features = 200)<\/code><\/pre>\n<\/div>\n<p>\u6211\u4eec\u628a\u5305\u52a0\u8f7d\u597d\u4e86\u4e4b\u540e\uff0c\u7136\u540e\u5bfc\u5165\u81ea\u5df1csv\u683c\u5f0f\u6587\u4ef6\uff0c\u7136\u540e\u5bfc\u5165\u6210\u529f\u540e\uff0c\u5c31\u53ef\u4ee5\u6b63\u5e38\u8fdb\u884c\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u4e86\uff01<\/p>\n<h2>\u8d28\u63a7\u4e0e\u8fc7\u6ee4\u4f4e\u8d28\u91cf\u7ec6\u80de<\/h2>\n<p>\u597d\u4e86\u5173\u4e8e\u6570\u636e\u4e0b\u8f7d\u548c\u5bfc\u5165\u5c31\u5b8c\u6210\u4e86\uff0c\u5c0f\u4f19\u4f34\u5feb\u53bb\u52a8\u624b\u8bd5\u8bd5\uff0c\u4e0b\u9762\u6211\u4eec\u5c31\u5f00\u59cb\u6b63\u5f0f\u5206\u6790\u4e86\uff01<\/p>\n<p>\u8fd9\u91cc\u5c0f\u679c\u628a\u5bfc\u5165\u6570\u636e\u5904\u7406\u4e00\u4e0b\uff1a<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code># \u67e5\u770bSeurat\u5bf9\u8c61\u7684\u57fa\u672c\u4fe1\u606f<\/code><code>data_seurat<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_YHoZWB8cXBgAWjezOiavwvp7JhWOxQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u4e2a\u5c31\u662f\u53ef\u4ee5\u770b\u5230\u6211\u4eec\u5bfc\u5165\u5355\u7ec6\u80de\u6570\u636e\u7684\u603b\u4f53<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>data_seurat[[\"percent.mt\"]]&lt;-PercentageFeatureSet(data_seurat,pattern = \"MT-\")<\/code><code>           <\/code><code>VlnPlot(data_seurat,features = c(\"nCount_RNA\",\"nFeature_RNA\",\"percent.mt\"))<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/16_pP8sv9aDHfsHhuPAFM7DULBWjsyalA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u6211\u4eec\u4ee5\u4e0d\u540c\u5f62\u5f0f\u5c55\u793a\u770b\u770b\u57fa\u56e0\u6570\u636e\u90a3\u4e9b\u7ec6\u80de\uff0c\u6bd4\u5982\u7ebf\u7c92\u4f53\u7b49<\/p>\n<p>\u7136\u540e\u6211\u4eec\u8981\u5254\u9664\uff0c<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>plot1&lt;-FeatureScatter(data_seurat,feature1 = \"nCount_RNA\",feature2 = \"percent.mt\")<\/code><code>plot2&lt;-FeatureScatter(data_seurat,feature1 = \"nCount_RNA\",feature2 = \"nFeature_RNA\")<\/code><code>CombinePlots(plots = list(plot1,plot2))    <\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/17_vOH08ZhDC9ACu7tHNPR0ibcGGaZbjg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\">\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/p>\n<p>\u5254\u9664\u60c5\u51b5\uff0c\u8fd9\u4e2a\u65e0\u5173\u7d27\u8981\uff0c<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc&lt;-subset(data_seurat,subset = nFeature_RNA&gt;200 &amp; nFeature_RNA&lt;2500 &amp; percent.mt&lt;5)<\/code><\/pre>\n<\/div>\n<p>\u8fd9\u4e2a\u6839\u636e\u5c0f\u4f19\u4f34\u81ea\u5df1\u7684\u60c5\u51b5\u53bb\u9009\u62e9\uff0c\u8303\u56f43000\u8fd8\u67095000 \u8fd8\u6709\u6700\u5c0f\u4e3a200\u8fd8\u662f\u591a\u5c11\uff0c\u5c0f\u4f19\u4f34\u53ef\u4ee5\u6839\u636e\u81ea\u8eab\u60c5\u51b5\uff0c<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>ncol(as.data.frame(pbmc[[\"RNA\"]]@counts))<\/code><code>pbmc&lt;-NormalizeData(pbmc,normalization.method = \"LogNormalize\",scale.factor = 10000)#\u5bf9\u6bcf\u4e2a\u7ec6\u80de\u6807\u51c6\u5316.<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/18_TSCIxmZuhOUdFm06jEzBJxRoXhic6w.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u91cc\u6211\u4eec\u5bf9\u6bcf\u4e2a\u7ec6\u80de\u90fd\u8fdb\u884c\u6807\u51c6\u5316\uff0c \u00a0 \u00a0<\/p>\n<h2>\u6807\u51c6\u5316\u3001\u964d\u7ef4\u548c\u805a\u7c7b<\/h2>\n<p>\u8fd9\u6b21\u5c0f\u679c\u7ee7\u7eed\u6559\u5c0f\u4f19\u4f34\u5bf9\u6570\u636e\u5904\u7406\uff0c\u8fd8\u6709\u6211\u4eec\u7684\u91cd\u5934\u620f\u5bf9\u5355\u7ec6\u80de\u6ce8\u91ca\uff0c\u4e0b\u9762\u6211\u4eec\u5f00\u59cb\u5427<\/p>\n<p>\u4e0a\u6b21\u6211\u4eec\u5904\u7406\u5230\uff0c<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/19_j2S19L1DBXQ6IBEPAR1GIylKTOdfkA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u5bf9\u6bcf\u4e2a\u7ec6\u80de\u90fd\u8fdb\u884c\u4e86\u6807\u51c6\u5316\uff0c\u4e0b\u9762\u6211\u4eec\u5c31\u662f\u8be5\u5bfb\u627e\u9ad8\u53d8\u7684\u57fa\u56e0\uff0c\u8fd9\u6837\u624d\u80fd\u627e\u5230\u4e0e\u6211\u4eec\u6574\u4f53\u5355\u7ec6\u80de\u76f8\u5173\u7684\u57fa\u56e0\u4e4b\u95f4\u7684\u5173\u7cfb\uff0c\u6765\u770b\u770b\u5982\u4f55\u5bfb\u627e<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#\u5bfb\u627e\u9ad8\u53d8\u57fa\u56e0<\/code><code>pbmc&lt;-FindVariableFeatures(pbmc,selection.method = \"vst\",nfeatures = 2000)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/20_Jz5QNyp4icBqArPJ3WXj3DhOg6viaQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u7136\u540e\u6211\u4eec\u8fdb\u884c<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#PCA<\/code><code>top10&lt;-head(VariableFeatures(pbmc))<\/code><\/pre>\n<\/div>\n<p>\u8fd9\u884c\u4ee3\u7801\u6211\u4eec\u67e5\u770b\u4e00\u4e0b\u524d\u5341\u4e2a\u7684\u9ad8\u53d8\u57fa\u56e0\uff0c\u53ef\u4ee5\u53d1\u73b0\u6211\u7684\u8fd9\u4e2a\u53ea\u67096\u4e2a\u9ad8\u53d8\u57fa\u56e0\uff0c\u53ef\u80fd\u6211\u9009\u53d6\u7684\u6570\u503c\u6bd4\u8f83\u5c11\uff0c\u4e0d\u8fc7\u4e0d\u5f71\u54cd<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/21_N5BuVUfqnOyEDoJvF95r1BUeoOXg8Q.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u6211\u4eec\u7ee7\u7eed\u5f80\u4e0b\u8d70<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>plot1&lt;-VariableFeaturePlot(pbmc)<\/code><code>plot2&lt;-LabelPoints(plot = plot1,points=top10,repel=T)<\/code><code>plot1    <\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/22_n8Xqq5lm8ddj9OFibibo6J1iaC1Dzg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>plot2 \u00a0 \u00a0<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/23_8vZJSeyibHibNicZIrbuVdv5aaZAhw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u628a\u6211\u4eec\u627e\u5230\u7684\u9ad8\u53d8\u57fa\u56e0\u653e\u5728\u706b\u5c71\u56fe\u4e0a\u9762\uff0c\u6211\u4eec\u5bfb\u627e\u9ad8\u53d8\u57fa\u56e0\u4e5f\u662f\u4e3a\u4e86\u5728\u540e\u7eed\u5bfb\u627e\u7ec6\u80de\u4e9a\u7fa4\u7684\u65f6\u5019\u5206\u79bb\u6709\u7528\uff0c\u6211\u4eec\u540e\u7eed\u518d\u8bf4\uff0c\u4e0b\u9762\u6211\u4eec\u5bf9\u57fa\u56e0\u8fdb\u884c\u6807\u51c6\u5316\uff0c\u548c\u4e0a\u9762\u4e0d\u540c\u8fd9\u6b21\u662f\u5bf9\u57fa\u56e0<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>all.genes&lt;-rownames(pbmc)<\/code><code>pbmc&lt;-ScaleData(pbmc,features = all.genes)#\u6bcf\u79cd\u57fa\u56e0\u5728\u7ec6\u80de\u4e2d\u7684\u6807\u51c6\u5316<\/code><code>pbmc &lt;- ScaleData(pbmc, vars.to.regress = \"percent.mt\")<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/24_hdzqWSHDT1mPthCSQEY8HVs2rFqFwA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"> \u00a0 \u00a0<\/p>\n<p>\u8fd9\u91cc\u5206\u6790\u597d\u4e86\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u540e\u7eed\u5206\u6790\uff0c\u5bf9\u7ec6\u80de\u8fdb\u884c\u805a\u7c7b\uff1a<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc&lt;-RunPCA(pbmc,features = VariableFeatures(object = pbmc))<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/25_tSdricRsp00R0ViaufOlibno4kEXyg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u5728\u505a\u4e00\u4e2aPCA\u5206\u6790\uff0c\u770b\u770b\u4e0d\u540c\u7c7b\u4e4b\u95f4\u7684\u5173\u8054\u00a0 \u00a0 \u00a0 \u00a0\u00a0\u00a0<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>print(pbmc[[\"pca\"]],dims=1:5,nfeatures=5)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/26_ibm2BMicr8BQbDia1YqtbicQtEUSPw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>VizDimLoadings(pbmc,dims = 1:2,reduction = \"pca\")<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/27_jRGKOiakaygCWORpVAodCEDxLFAv0A.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>DimPlot(pbmc,reduction = \"pca\")<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/28_WNkCfJMOC39Y4MRiaZaicjsbxq5VdA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>DimHeatmap(pbmc,dims=1,cells=500,balanced = T)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/29_8WQj8Rfvp6cRN8JvibPJo2RboWGibg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u4e2a\u5c31\u53ef\u4ee5\u770b\u5230\u6bcf\u4e2a\u57fa\u56e0\u5728\u4e0d\u540c\u7684\u4e9a\u7fa4\u4e4b\u95f4\u7684\u8868\u8fbe\u5982\u4f55\uff0c\u8fd8\u53ef\u4ee5\u5206\u5f00\u6765\u770b<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>DimHeatmap(pbmc,dims = 1:15,cells=500,balanced = T)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/30_f6qeE4nwsj8wqNibGt0qKZIhVlUdGA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u4e2a\u5c31\u53ef\u4ee5\u770b\u51fa\u6765\u4e00\u4e9b\u57fa\u56e0\u5728\u4e0d\u540c\u4e9a\u7fa4\u7684\u8868\u8fbe\u91cf\uff0c\u4f46\u662f\u6211\u4eec\u4e0d\u77e5\u9053\u5206\u591a\u5c11\u5408\u9002\u5462\uff0c\u8fd9\u91cc\u5c31\u9700\u8981\u8fdb\u884c\u540e\u7eed\u7684\u5206\u6790\uff1a<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc&lt;-JackStraw(pbmc,num.replicate = 100)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/31_SmtbF6HXiazyAicVmouAjpEic0Uibg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u4e00\u6b65\u5c31\u662f\u5206\u79bb\u5206\u6790\uff0c\u5c0f\u4f19\u4f34\u8010\u5fc3\u7b49\u5f85\u4e00\u4e0b<\/p>\n<p>\u5c31\u662f\u5728\u5bfb\u627e\u6700\u4f73\u5206\u7fa4<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc&lt;-ScoreJackStraw(pbmc,dims=1:20)<\/code><code>JackStrawPlot(pbmc,dim=1:20)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/32_u0310oJ6rJib6HpjibTCNrOHicjSfg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/33_8ukMaVLp0Ba3wNSxDF0ZaX9hTpfTlw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u4e2a\u5c31\u662f\u4e0d\u540c\u4e9a\u7fa4\u7684P\u503c\u60c5\u51b5\uff0c<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>ElbowPlot(pbmc)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/34_8JdYTM1J9TnCUKTf9R5CIdnmicyXJA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u4e2a\u788e\u77f3\u56fe\u6211\u4eec\u5c31\u53ef\u4ee5\u770b\u770b\u5728\u54ea\u91cc\u5e73\u7f13\u6211\u4eec\u5c31\u9009\u62e9\u54ea\u91cc\uff0c\u5c0f\u56fe\u8fd9\u5f20\u56fe\u5c31\u9009\u62e917\u6216\u800515\u90fd\u53ef\u4ee5<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc&lt;-FindNeighbors(pbmc,dims=1:17)<\/code><code>pbmc&lt;-FindClusters(pbmc,resolution = 1.2)#0.4-1.2\u4e4b\u95f4\uff0c\u6570\u503c\u8d8a\u5927\u5206\u7fa4\u8d8a\u591a<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/35_A4Mdj51eMP5Xxtj9u8lhTkicnUD6cA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>head(Idents(pbmc), 5)   \u00a0<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/36_DJOdN37rchHVdm499qazkoKJPlDpzg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u91cc\u53ef\u4ee5\u770b\u51fa\u6765\u6211\u4eec\u5206\u4e869\u4e2a\u4e9a\u7fa4<\/p>\n<p>\u7136\u540e\u6211\u4eec\u8fdb\u884c\u964d\u7ef4<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc&lt;-RunUMAP(pbmc,dims=1:17)#\u4e00\u79cd\u964d\u7ef4\u65b9\u6cd5<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/37_cK6fhXf4cz0ia9Pn7iadTiajkjyb2Q.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>DimPlot(pbmc,reduction = \"umap\")#umap\u7528\u4e8e\u5927\u578b\u6570\u636e<\/code><\/pre>\n<\/div>\n<p>\u7136\u540e\u540e\u9762\u6211\u4eec\u5c31\u8981\u8fdb\u884c\u964d\u7ef4\u7ed8\u5236\u56fe\uff0c \u00a0 \u00a0<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/38_2SbsbVZcJrNlzEknzAA98tGso7OEjA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u91cc\u7528\u7684\u662fumap\u65b9\u5f0f\u8fdb\u884c\u53ef\u89c6\u5316\u964d\u7ef4\u7ed3\u679c\uff0c\u5bf9\u4e8e\u5927\u6570\u636e\u6765\u8bf4\u662f\u6bd4\u8f83\u9002\u7528\u7684\uff0c\u6211\u4eec\u8fd8\u53ef\u4ee5\u8fdb\u884c\u5176\u4ed6\u65b9\u5f0f\uff0c\u6bd4\u5982tsne\uff0c\u9002\u5408\u5c0f\u6570\u636e<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc&lt;-RunTSNE(pbmc,dims=1:17)#\u53e6\u4e00\u79cd\u964d\u7ef4\u65b9\u6cd5<\/code><code>DimPlot(pbmc,reduction = \"tsne\")#tsne\u7528\u4e8e\u5c0f\u578b\u6570\u636e\uff0c\u5206\u79bb\u6548\u679c\u66f4\u597d<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/39_BicCjysrVZ9LS2KtLqPq6ORI8vr8YA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u4e2a\u5c31\u53ef\u4ee5\u770b\u51fa\u6765\uff0c\u5c0f\u679c\u7684\u6570\u636e\u662f\u5c0f\u578b\u6570\u636e\uff0c\u6240\u4ee5\u5462\uff0c\u5728\u4f7f\u7528tsne\u65b9\u5f0f\u7684\u66f4\u660e\u663e\u7684\u5206\u79bb\u5355\u7ec6\u80de\u4e9a\u7fa4<\/p>\n<p>\u6700\u540e\u5462\u5c31\u662f\u9700\u8981\u627e\u5230\u6211\u4eec\u7684\u5404\u7c7b\u7684\u5173\u952e\u57fa\u56e0<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#\u627e\u5404\u7c7b\u5173\u952e\u57fa\u56e0<\/code><code>pbmc.markers&lt;-FindAllMarkers(pbmc,only.pos = T,min.pct = 0.25,logfc.threshold = 0.25)#\u5bfb\u627e\u6240\u6709\u7c7b\u7684makers\u57fa\u56e0    <\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/40_dtX5AH8WWRxfT5MWyvkIsV319KZFdg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc.markers%&gt;%group_by(cluster) %&gt;% top_n(n=2,wt=avg_log2FC)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/41_FvkzfwrndScaeB9yDZLVzaTWojwiaQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u5bf9\u7ed3\u679c\u5c55\u793a\uff0c\u4e00\u4e9b\u5173\u952e\u57fa\u56e0\uff0c\u6211\u4eec\u53ef\u4ee5\u9009\u62e9\u524d\u5341\u540d\u7684\u5c55\u793a\u5176\u5728\u5355\u7ec6\u80de\u4e9a\u7fa4\u4e2d\u7684\u5f62\u5f0f\u00a0 \u00a0 \u00a0 \u00a0\u00a0\u00a0<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>VlnPlot(pbmc,features = c(\"GPX2\",\"AKR1C2\"),slot = \"counts\",log=T)<\/code><\/pre>\n<\/div>\n<p>\u5c0f\u56fe\u8fd9\u91cc\u5bf9\u524d\u4e24\u540d\u7684\u57fa\u56e0\u8fdb\u884c\u5c55\u793a \u00a0 \u00a0<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/42_PyjwmPSboYJ0UDnFErlqPCeibxFbag.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>FeaturePlot(pbmc,features = c(\"GPX2\"),reduction = \"tsne\")<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/43_I6S6nUhnb65icZx6pYm4boSt4LK59w.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u91cc\u5c31\u53ef\u4ee5\u5f88\u660e\u663e\u7684\u770b\u51faGPX2\u8fd9\u4e2a\u57fa\u56e0\u5728\u90a3\u4e9b\u7ec6\u80de\u4e2d\u5360\u6bd4\u6700\u591a\uff0c<\/p>\n<p>reduction = &#8220;tsne&#8221;\u8fd9\u4e2a\u53c2\u6570\u53ef\u4ee5\u6539\u53d8\u7ed8\u56fe\u7684\u65b9\u5f0f\uff0c<\/p>\n<p>\u7136\u540e\u6211\u4eec\u5bf9\u524d\u5341\u540d\u7684\u8fdb\u884c\u4fdd\u5b58<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>top10&lt;-pbmc.markers%&gt;%group_by(cluster) %&gt;% top_n(n=10,wt=avg_log2FC)<\/code><code>DoHeatmap(pbmc,features = top10$gene)+NoLegend()<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/44_8m6UrZrIyuuL1DBBONENFg0nuMNe3A.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u91cc\u5bf9\u5173\u952e\u57fa\u56e0\u8868\u8fbe\u91cf\u8fdb\u884c\u70ed\u56fe\u7684\u7ed8\u5236\uff0c\u770b\u770b\u8fd9\u4e9b\u57fa\u56e0\u5728\u90a3\u4e2a\u4e9a\u7fa4\u4e2d\u8868\u8fbe\u5982\u4f55\uff0c<\/p>\n<p>saveRDS(pbmc,&#8221;pbmc.rds&#8221;)<\/p>\n<p>\u6700\u540e\u6211\u4eec\u4fdd\u5b58\u4e00\u4e0b\u8fd9\u4e9b\u4fe1\u606f\uff0c<\/p>\n<h2>\u4f7f\u7528 SingleR \u5b8c\u6210\u7ec6\u80de\u6ce8\u91ca<\/h2>\n<p>\u7136\u540e\u6211\u4eec\u5bf9\u8fd9\u4e9b\u7ec6\u80de\u8fdb\u884c\u6ce8\u91ca\uff0c\u8fd9\u91cc\u6211\u4eec\u4f7f\u7528SingleR\u5305\u8fdb\u884c\u81ea\u52a8\u6ce8\u91ca\uff0c\u6bd4\u8f83\u65b9\u4fbf\uff0c\u5c0f\u679c\u4ee5\u53ca\u628a\u8fd9\u4e2a\u6570\u636e\u7684\u4fe1\u606f\u4e0b\u8f7d\u4e0b\u6765\u4e86\uff0c\u5c0f\u4f19\u4f34\u53ef\u4ee5\u81ea\u884c\u53bb\u540e\u53f0\u9886\u53d6<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>library(SingleR)<\/code><code>#BiocManager::install(\"celldex\")<\/code><code>library(celldex)    <\/code><code>library(Seurat)<\/code><code>library(pheatmap)<\/code><\/pre>\n<\/div>\n<p>\u52a0\u8f7d\u4e00\u4e0b\u5305\uff0c\u6211\u4eec\u8fdb\u884c\u5355\u7ec6\u80de\u6ce8\u91ca<\/p>\n<p>##\u4e0b\u8f7d\u6ce8\u91ca\u6570\u636e\u5e93\uff0c\u8fd9\u91cc\u627e\u5c0f\u679c\u9886\u53d6\u4e0e\u559c\u7231\u4e0b\u8f7d\u597d\u7684\u6570\u636e\u5e93\u4fe1\u606f<\/p>\n<p>\u5c0f\u4f19\u4f34\u4e5f\u53ef\u4ee5\u81ea\u884c\u53bb\u4e0b\u8f7d\uff0c\u4e0d\u8fc7\u4e00\u822c\u4f1a\u56e0\u4e3a\u7f51\u7edc\u95ee\u9898\u5931\u8d25\uff0c<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>hpca.se &lt;- HumanPrimaryCellAtlasData()<\/code><code>hpca.se<\/code><code>           <\/code><code>           <\/code><code>#\u76f4\u63a5load\u4e0b\u8f7d\u597d\u7684\u6570\u636e\u5e93<\/code><\/pre>\n<\/div>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>load(\"HumanPrimaryCellAtlas_hpca.se_human.RData\")<\/code><code>           <\/code><code>load(\"BlueprintEncode_bpe.se_human.RData\")<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/45_cgvLsRrUGqp68nebfHrADeV3rzO4VQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\">\u00a0\u00a0\u00a0\u00a0<\/p>\n<p>pbmc#\u4e0a\u9762\u5c0f\u679c\u5904\u7406\u597d\u7684\u5355\u7ec6\u80de\u4fe1\u606f<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/46_9ozS4MXjwDLfLiaoDuHNYAguG27lGA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>meta=pbmc@meta.data #pbmc\u7684meta\u6587\u4ef6\uff0c\u5305\u542b\u4e86seurat\u7684\u805a\u7c7b\u7ed3\u679c    <\/code><code>head(meta)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/47_q1YJmXNRGnwHiawvibNZxXzhvKic1Q.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u91cc\u67e5\u770b\u4e00\u4e0b\u4fe1\u606f<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>plot1 &lt;- DimPlot(pbmc, reduction = \"umap\", label = TRUE)<\/code><code>           <\/code><code>plot2&lt;-DimPlot(pbmc, reduction = \"tsne\",<\/code><code>               label = TRUE)<\/code><code>plot1 + plot2<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/48_hk4O6GcVWA9nQ5nZaicKE4XbNibXxw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u7136\u540e\u6211\u4eec\u5c31\u5f00\u59cb\u6ce8\u91ca\u5427\uff01<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#\u8fdb\u884csingleR\u6ce8\u91ca<\/code><code>pbmc_for_SingleR &lt;- GetAssayData(pbmc, slot=\"data\") ##\u83b7\u53d6\u6807\u51c6\u5316\u77e9\u9635<\/code><code>pbmc.hesc &lt;- SingleR(test = pbmc_for_SingleR, ref = hpca.se, labels = hpca.se$label.main) #<\/code><code>pbmc.hesc<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/49_MhHTwlQyT8q1BoTaMr7ic4vfBWhxlw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#seurat \u548c singleR\u7684table\u8868<\/code><code>table(pbmc.hesc$labels,meta$seurat_clusters)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/50_LmSzuSpDNLzbEX57Y5mpVrE0ChJE1A.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u6ce8\u91ca\u7ed3\u679c<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#umap\u56fe<\/code><code>           <\/code><code>pbmc@meta.data$labels &lt;-pbmc.hesc$labels<\/code><code>           <\/code><code>           <\/code><code>print(DimPlot(pbmc, group.by = c(\"seurat_clusters\", \"labels\"),reduction = \"umap\"))<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/51_ia1Micpia4WMSDUWz4ic1Ixu3VWB1A.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u8fd9\u91cc\u6211\u4eec\u6ce8\u91ca\u5b8c\u6210\u4e86\uff01<\/p>\n<h2>\u591a\u6570\u636e\u5e93\u9a8c\u8bc1\u6ce8\u91ca\u7ed3\u679c<\/h2>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>##\u591a\u4e2a\u6570\u636e\u5e93\u6ce8\u91ca<\/code><code>pbmc3 &lt;- pbmc<\/code><code>           <\/code><code>pbmc3.hesc &lt;- SingleR(test = pbmc_for_SingleR, ref = list(BP=bpe.se, HPCA=hpca.se),<\/code><code>                      labels = list(bpe.se$label.main, hpca.se$label.main))<\/code><code>table(pbmc3.hesc$labels,meta$seurat_clusters)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/52_apfF83IxmFfSanrPAPTtrxAxXgFcUg.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>pbmc3@meta.data$labels &lt;-pbmc3.hesc$labels<\/code><code>           <\/code><\/pre>\n<\/div>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>print(DimPlot(pbmc3, group.by = c(\"seurat_clusters\", \"labels\"),reduction = \"tsne\"))<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/53_FEVJ4ibvQVfEicqFQnPrP2VpYEAf4w.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#\u7ed3\u679c\u8bca\u65ad<\/code><code>print(plotScoreHeatmap(pbmc.hesc))<\/code><code>           <\/code><code>plotDeltaDistribution(pbmc.hesc, ncol = 3)<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/54_JdnAnlHXu2F0CslH0vNXBrfMHicS5g.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#cluster\u7ed3\u679c\u5bf9\u6bd4<\/code><code>           <\/code><code>tab &lt;- table(label = pbmc.hesc$labels,<\/code><code>            <\/code><code>             cluster = meta$seurat_clusters)<\/code><code>           <\/code><code>pheatmap(log10(tab + 10))<\/code><\/pre>\n<\/div>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/55_cmcubZuSw3WM9ic1WH6RFjicWTPiaA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p>\u597d\u4e86\uff0c\u5230\u6b64\u6211\u4eec\u7684\u5355\u7ec6\u80de\u5165\u95e8\u5b66\u4e60\u7684\u6559\u7a0b\u5c31\u7ed3\u675f\u4e86\uff0c\u5c0f\u4f19\u4f34\u8981\u597d\u597d\u6d88\u5316\u4e00\u4e0b\uff0c\u5bf9\u6b64\u6570\u636e\u8fdb\u884c\u4eb2\u624b\u64cd\u4f5c\uff01<\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/56_VmRkv7tSNKliafDnsuFR7BoeDgBrww.jpg?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n<p><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/57_FbEg9fibwQicL8l2ExKOZZTmAHXabQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5c0f\u679c\u7684\u5355\u7ec6\u80de\u5206\u6790\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\u624b\u628a\u624b\u6559\u4f60\u4ece\u5355\u7ec6\u80de\u6570\u636e\u4e0b\u8f7d\u548c\u5904\u7406\u5230\u5355\u7ec6\u80de\u6ce8\u91ca\uff01\uff01 \u5c0f\u56fe \u751f\u4fe1\u679c 2024-01-04 19:02:54 \u8f6c\u81ea\u516c\u4f17\u53f7\uff1a\u751f\u4fe1\u56fehttp:\/\/mp.weixin.qq.com\/s?__biz=MzkxODUxNDgzNA==&#038;mid=22474\u2026<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_post_was_ever_published":false},"categories":[1,71],"tags":[],"class_list":["post-58633","post","type-post","status-publish","format-standard","hentry","category-part","category-single-cell"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/58633","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/comments?post=58633"}],"version-history":[{"count":3,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/58633\/revisions"}],"predecessor-version":[{"id":65434,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/58633\/revisions\/65434"}],"wp:attachment":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/media?parent=58633"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/categories?post=58633"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/tags?post=58633"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}