{"id":68216,"date":"2026-11-14T20:24:57","date_gmt":"2026-11-14T12:24:57","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=68216"},"modified":"2026-11-14T20:24:57","modified_gmt":"2026-11-14T12:24:57","slug":"nichenet-ligand-ranking-receiver-background-genes","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/nichenet-ligand-ranking-receiver-background-genes\/","title":{"rendered":"NicheNet \u914d\u4f53\u6392\u4e86\u7b2c\u4e00\uff0c\u5148\u770b\u770b\u63a5\u6536\u7ec6\u80de\u7684\u80cc\u666f\u57fa\u56e0\u9009\u5bf9\u6ca1\u6709"},"content":{"rendered":"
\n

\u5728\u5904\u7406\u540e\u7684\u6210\u7ea4\u7ef4\u7ec6\u80de\u91cc\u627e\u51fa\u4e00\u767e\u4e2a\u4e0a\u8c03\u57fa\u56e0\uff0c\u60f3\u77e5\u9053\u90bb\u8fd1\u514d\u75ab\u7ec6\u80de\u5206\u6ccc\u7684\u54ea\u79cd\u914d\u4f53\u53ef\u80fd\u4fc3\u6210\u8fd9\u7ec4\u53d8\u5316\u3002NicheNet \u80fd\u628a\u5019\u9009\u914d\u4f53\u548c\u63a5\u6536\u7ec6\u80de\u7684\u8f6c\u5f55\u54cd\u5e94\u8054\u7cfb\u8d77\u6765\u3002\u5b83\u7528\u65e2\u6709\u914d\u4f53\u3001\u53d7\u4f53\u3001\u80de\u5185\u4fe1\u53f7\u548c\u8c03\u63a7\u77e5\u8bc6\u6784\u6210\u7684\u5148\u9a8c\u6a21\u578b\uff0c\u68c0\u67e5\u4e00\u4e2a\u914d\u4f53\u7684\u9884\u6d4b\u9776\u70b9\u80fd\u5426\u89e3\u91ca\u5173\u6ce8\u7684\u57fa\u56e0\u3002\u7ed3\u679c\u6700\u5bb9\u6613\u88ab\u5ffd\u7565\u7684\u4e00\u5217\u662f\u80cc\u666f\u57fa\u56e0\u3002\u5b83\u51b3\u5b9a\u54ea\u4e9b\u57fa\u56e0\u66fe\u6709\u673a\u4f1a\u88ab\u9009\u4e3a\u54cd\u5e94\u57fa\u56e0\uff0c\u4e5f\u51b3\u5b9a\u4e00\u4e2a\u770b\u8d77\u6765\u6f02\u4eae\u7684\u547d\u4e2d\u6bd4\u4f8b\u5e94\u5f53\u548c\u4ec0\u4e48\u6bd4\u8f83\u3002<\/p>\n

\u5148\u5b9a\u4e49\u63a5\u6536\u7aef\uff0c\u518d\u5217\u80fd\u88ab\u68c0\u9a8c\u7684\u57fa\u56e0<\/h2>\n

\u628a\u7814\u7a76\u95ee\u9898\u5199\u6210\u4e00\u53e5\u5177\u4f53\u7684\u8bdd\uff0c\u6bd4\u5982\u6bd4\u8f83\u540c\u4e00\u79cd\u6210\u7ea4\u7ef4\u7ec6\u80de\u5728\u523a\u6fc0\u524d\u540e\u7684\u8868\u8fbe\uff0c\u5019\u9009\u4fe1\u53f7\u6765\u81ea\u540c\u4e00\u7ec4\u7ec7\u91cc\u7684\u5355\u6838\u7ec6\u80de\u3002\u5148\u5728\u63a5\u6536\u7fa4\u5185\u786e\u5b9a\u6761\u4ef6\u5dee\u5f02\uff0c\u6838\u5bf9\u5b9e\u9a8c\u8bbe\u8ba1\u548c\u4f9b\u4f53\u91cd\u590d\u3002\u82e5\u76f4\u63a5\u62ff\u5355\u6838\u7ec6\u80de\u4e0e\u6210\u7ea4\u7ef4\u7ec6\u80de\u7684\u5dee\u5f02\u4f5c\u54cd\u5e94\u57fa\u56e0\uff0c\u7ed3\u679c\u4f1a\u4f18\u5148\u53cd\u6620\u4e24\u4e2a\u8c31\u7cfb\u672c\u8eab\u6709\u4f55\u4e0d\u540c\u3002\u5b83\u56de\u7b54\u4e0d\u4e86\u523a\u6fc0\u4e4b\u540e\u6210\u7ea4\u7ef4\u7ec6\u80de\u65b0\u51fa\u73b0\u4e86\u54ea\u4e9b\u4e0b\u6e38\u53d8\u5316\u3002\u4e00\u4e2a\u4f9b\u4f53\u7684\u591a\u4e2a\u7ec6\u80de\u4e5f\u4e0d\u80fd\u5f53\u6210\u591a\u4efd\u72ec\u7acb\u523a\u6fc0\u5b9e\u9a8c\u3002<\/p>\n

\u80cc\u666f\u539f\u5219\u4e0a\u5e94\u6765\u81ea\u63a5\u6536\u7fa4\u4e2d\u786e\u5b9e\u6709\u673a\u4f1a\u8fdb\u5165\u8fd9\u6b21\u6bd4\u8f83\u7684\u57fa\u56e0\uff0c\u518d\u4e0e\u914d\u4f53\u2013\u9776\u6807\u77e9\u9635\u652f\u6301\u7684\u57fa\u56e0\u53d6\u4ea4\u96c6\u3002\u76ee\u6807\u54cd\u5e94\u96c6\u5408\u4e5f\u8981\u505a\u540c\u6837\u7684\u540d\u5b57\u6620\u5c04\uff0c\u4e14\u5e94\u5c5e\u4e8e\u80cc\u666f\u3002\u82e5\u5019\u9009\u8868\u6709\u4e00\u767e\u884c\uff0c\u6620\u5c04\u540e\u53ea\u5269\u516d\u5341\u4e2a\uff0c\u5c31\u62a5\u544a\u5b9e\u9645\u7528\u4e8e\u8bc4\u5206\u7684\u662f\u516d\u5341\u4e2a\uff0c\u53e6\u67e5\u4e22\u5931\u7684\u56db\u5341\u4e2a\u662f\u65e7\u540d\u3001\u91cd\u590d\u9879\u3001\u7269\u79cd\u4e0d\u5339\u914d\uff0c\u8fd8\u662f\u6a21\u578b\u672c\u8eab\u8986\u76d6\u4e0d\u5230\u3002\u628a\u53c2\u8003\u57fa\u56e0\u7ec4\u6240\u6709\u57fa\u56e0\u90fd\u76f4\u63a5\u4f5c\u4e3a\u80cc\u666f\uff0c\u4f1a\u628a\u8bb8\u591a\u5b9e\u9a8c\u4ece\u672a\u80fd\u6d4b\u5230\u7684\u9879\u76ee\u53d8\u6210\u8868\u9762\u4e0a\u7684\u201c\u9634\u6027\u201d\u3002NicheNet \u4f5c\u8005\u7684\u914d\u4f53\u6d3b\u6027\u5206\u6790\u793a\u4f8b<\/a><\/p>\n

\u7528\u547d\u4e2d\u7387\u624b\u7b97\u4e24\u4e2a\u4e0d\u540c\u7684\u80cc\u666f<\/h2>\n

\u5047\u8bbe\u5728\u4e00\u767e\u4e2a\u53ef\u8bc4\u4f30\u57fa\u56e0\u4e2d\u6709\u5341\u4e2a\u771f\u6b63\u88ab\u5217\u5165\u672c\u6b21\u54cd\u5e94\u96c6\u5408\u3002\u67d0\u5019\u9009\u914d\u4f53\u9884\u6d4b\u6392\u540d\u7b2c\u4e00\u5230\u7b2c\u4e94\u7684\u57fa\u56e0\u4e2d\uff0c\u4e09\u4e2a\u5c5e\u4e8e\u8fd9\u5341\u4e2a\u54cd\u5e94\u57fa\u56e0\u3002\u8fd9\u65f6\u53d6\u524d\u4e94\u540d\u7684\u7cbe\u786e\u7387\u662f\u4e94\u5206\u4e4b\u4e09\uff0c\u53ec\u56de\u7387\u662f\u5341\u5206\u4e4b\u4e09\u3002\u968f\u673a\u4ece\u8fd9\u4e2a\u80cc\u666f\u91cc\u62bd\u57fa\u56e0\uff0c\u9884\u671f\u7684\u9633\u6027\u6bd4\u4f8b\u662f\u4e00\u6210\u3002\u4e0b\u9762\u53ea\u4f5c\u6392\u540d\u76f4\u89c9\u6f14\u7b97\uff0c\u8f6f\u4ef6\u5b9e\u9645\u4e0a\u4f1a\u6cbf\u591a\u4e2a\u6392\u540d\u622a\u70b9\u8003\u5bdf\u7cbe\u786e\u7387\u4e0e\u53ec\u56de\u7387\uff0c\u5e76\u6709\u9488\u5bf9\u968f\u673a\u57fa\u7ebf\u7684\u6821\u6b63\u6307\u6807\u3002<\/p>\n

\n\n\n\n\n\n\n
\u60c5\u5f62<\/th>\n\u80cc\u666f\u4e2d\u54cd\u5e94\u57fa\u56e0\u5360\u6bd4<\/th>\n\u524d\u4e94\u540d\u547d\u4e2d<\/th>\n\u7cbe\u786e\u7387\u4e0e\u53ec\u56de\u7387<\/th>\n<\/tr>\n<\/thead>\n
\u4e00\u767e\u4e2a\u53ef\u8bc4\u4f30\u57fa\u56e0<\/td>\n10 \/ 100<\/td>\n3 \/ 5<\/td>\n60% \u4e0e 30%<\/td>\n<\/tr>\n
\u4ec5\u4fdd\u7559\u4e8c\u5341\u4e2a\u53ef\u8bc4\u4f30\u57fa\u56e0\uff0c\u4ecd\u6709\u5341\u4e2a\u9633\u6027<\/td>\n10 \/ 20<\/td>\n3 \/ 5<\/td>\n\u4ecd\u4e3a 60% \u4e0e 30%<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u540c\u6837\u547d\u4e2d\u4e09\u4e2a\uff0c\u5206\u91cf\u4e00\u6837\u5417\u3002\u6559\u5b66\u7b97\u4f8b\uff5c\u4e24\u4efd\u9762\u677f\u90fd\u4fdd\u7559\u4e86\u5341\u4e2a\u54cd\u5e94\u57fa\u56e0\uff0c\u524d\u4e94\u540d\u5747\u547d\u4e2d\u4e09\u4e2a\u300210
\u6559\u5b66\u7b97\u4f8b\uff5c\u4e24\u4efd\u9762\u677f\u90fd\u4fdd\u7559\u4e86\u5341\u4e2a\u54cd\u5e94\u57fa\u56e0\uff0c\u524d\u4e94\u540d\u5747\u547d\u4e2d\u4e09\u4e2a\u3002<\/figcaption><\/figure>\n

\u7b2c\u4e8c\u884c\u662f\u53e6\u4e00\u4e2a\u53d7\u9650\u9762\u677f\uff0c\u5047\u5b9a\u524d\u4e94\u540d\u548c\u5168\u90e8\u5341\u4e2a\u9633\u6027\u90fd\u6070\u597d\u4ecd\u7136\u4fdd\u7559\u3002\u53ea\u770b\u8868\u6700\u540e\u4e00\u5217\uff0c\u4e8c\u8005\u6ca1\u6709\u5dee\u522b\u3002\u5982\u679c\u518d\u95ee\u968f\u673a\u9009\u65f6\u4f1a\u547d\u4e2d\u591a\u5c11\uff0c\u7b2c\u4e8c\u4e2a\u80cc\u666f\u5df2\u6709\u4e00\u534a\u662f\u9633\u6027\uff0c\u89c2\u5bdf\u5230\u516d\u6210\u5c31\u6ca1\u6709\u7b2c\u4e00\u884c\u90a3\u4e48\u5f15\u4eba\u6ce8\u610f\u3002\u5b9e\u9645\u66f4\u6362\u80cc\u666f\u8fd8\u53ef\u80fd\u4f7f\u5019\u9009\u7684\u987a\u5e8f\u672c\u8eab\u53d1\u751f\u6539\u53d8\u3002\u4ec5\u51ed\u524d\u4e09\u4e2a\u547d\u4e2d\u65e0\u6cd5\u590d\u539f\u6574\u4e2a\u7cbe\u786e\u7387\u2013\u53ec\u56de\u7387\u66f2\u7ebf\uff0c\u66f4\u4e0d\u80fd\u628a\u90a3\u4e2a\u767e\u5206\u6570\u5f53\u6210\u914d\u4f53\u9020\u6210\u54cd\u5e94\u7684\u6982\u7387\u3002\u8fd9\u4e2a\u7ec3\u4e60\u7684\u7528\u9014\u662f\uff0c\u62ff\u5230\u522b\u4eba\u7ed9\u7684\u6392\u540d\u65f6\u5148\u8ffd\u95ee\u6240\u7528\u5206\u6bcd\u3002<\/p>\n

\u5c06\u914d\u4f53\u8868\u8fbe\u3001\u53d7\u4f53\u53ef\u7528\u548c\u9776\u70b9\u89e3\u91ca\u5206\u5f00<\/h2>\n

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\u4e0b\u4f8b\u5047\u5b9a\u5df2\u7ecf\u4ece\u5dee\u5f02\u68c0\u9a8c\u5f97\u5230\u63a5\u6536\u7aef\u7684\u54cd\u5e94\u5217\u8868\uff0c\u53e6\u6709\u5b9e\u9645\u68c0\u9a8c\u8fc7\u7684\u53ef\u8868\u8fbe\u57fa\u56e0\u3001\u6309\u53d1\u9001\u4e0e\u63a5\u6536\u6761\u4ef6\u9009\u51fa\u7684\u5019\u9009\u914d\u4f53\uff0c\u4ee5\u53ca\u540c\u4e00\u7269\u79cd\u7684\u5148\u9a8c\u77e9\u9635\u3002\u5148\u68c0\u67e5\u4ea4\u96c6\uff0c\u80fd\u5c06\u4e0d\u5c11\u201c\u8dd1\u5b8c\u5374\u6ca1\u6709\u7ed3\u679c\u201d\u7684\u95ee\u9898\u5b9a\u4f4d\u5230\u8f93\u5165\u3002\u5b9e\u9645\u5206\u6790\u5e94\u8bb0\u5f55\u76f8\u4ea4\u524d\u540e\u5206\u522b\u6709\u591a\u5c11\u9879\uff0c\u5e76\u4fdd\u7559\u6539\u53d8\u8fc7\u6ee4\u6807\u51c6\u65f6\u7684\u5b8c\u6574\u6392\u540d\u3002NicheNet \u9879\u76ee\u8bf4\u660e<\/a><\/p>\n

background <- intersect(unique(tested_in_receiver), rownames(ligand_target_matrix))\r\ngeneset <- intersect(unique(receiver_response), background)\r\nligands <- intersect(unique(candidate_ligands), colnames(ligand_target_matrix))\r\nstopifnot(length(geneset) > 0, length(geneset) < length(background),\r\n          length(ligands) > 0)\r\nranked <- nichenetr::predict_ligand_activities(\r\n  geneset = geneset, background_expressed_genes = background,\r\n  ligand_target_matrix = ligand_target_matrix, potential_ligands = ligands\r\n)\r\nhead(ranked[order(-ranked$aupr_corrected), ])\r\n<\/code><\/pre>\n
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