{"id":61782,"date":"2024-11-19T16:32:13","date_gmt":"2024-11-19T08:32:13","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61782"},"modified":"2024-11-19T16:32:13","modified_gmt":"2024-11-19T08:32:13","slug":"%e5%86%8d%e4%b8%8d%e4%bc%9a%e5%ae%89%e8%a3%85r%e5%8c%85%e4%bd%a0%e5%b0%b1out%e4%ba%86%e4%b8%80%e6%ac%a1%e5%ad%a6%e4%bc%9ar%e5%8c%85%e7%9a%84%e5%ae%89%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61782","title":{"rendered":"\u518d\u4e0d\u4f1a\u5b89\u88c5R\u5305\u4f60\u5c31out\u4e86!!!\u4e00\u6b21\u5b66\u4f1aR\u5305\u7684\u5b89\u88c5"},"content":{"rendered":"\n<p>\u5728\u751f\u7269\u4fe1\u606f\u5b66\u7684\u5b66\u4e60\u7814\u7a76\u548c\u53d1\u5c55\u4e2d\uff0cR \u8bed\u8a00\u56e0\u5176\u5f3a\u5927\u7684\u7edf\u8ba1\u5206\u6790\u548c\u6570\u636e\u53ef\u89c6\u5316\u80fd\u529b\uff0c\u6210\u4e3a\u751f\u7269\u7814\u7a76\u4eba\u5458\u7684\u91cd\u8981\u5de5\u5177\u3002R \u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u529f\u80fd\uff0c\u80fd\u591f\u5904\u7406\u5927\u89c4\u6a21\u7684\u751f\u7269\u6570\u636e\u96c6\uff0c\u8fdb\u884c\u590d\u6742\u7684\u7edf\u8ba1\u5efa\u6a21\uff0c\u4ee5\u53ca\u751f\u6210\u9ad8\u8d28\u91cf\u7684\u56fe\u5f62\uff0c\u8fd9\u4f7f\u5f97\u5b83\u5728\u57fa\u56e0\u7ec4\u5b66\u3001\u8f6c\u5f55\u7ec4\u5b66\u548c\u86cb\u767d\u8d28\u7ec4\u5b66\u7b49\u9886\u57df\u5f97\u5230\u5e7f\u6cdb\u5e94\u7528\u3002<\/p>\n\n\n\n<p>\u7136\u800c\uff0cR \u7684\u5f3a\u5927\u4e4b\u5904\u4e0d\u4ec5\u5728\u4e8e\u5176\u57fa\u7840\u529f\u80fd\uff0c\u8fd8\u4f53\u73b0\u5728\u5176\u4e30\u5bcc\u7684\u5305\u751f\u6001\u7cfb\u7edf\u3002R \u5305\u662f\u4e00\u4e9b\u9884\u5148\u7f16\u5199\u7684\u51fd\u6570\u548c\u6570\u636e\u96c6\u5408\uff0c\u65e8\u5728\u89e3\u51b3\u7279\u5b9a\u7684\u751f\u7269\u4fe1\u606f\u5b66\u95ee\u9898\u3002\u4f8b\u5982\uff0c\u5e38\u7528\u7684 Bioconductor \u5305\u4e13\u95e8\u4e3a\u751f\u7269\u6570\u636e\u5206\u6790\u8bbe\u8ba1\uff0c\u6db5\u76d6\u4e86\u4ece\u6570\u636e\u9884\u5904\u7406\u5230\u7ed3\u679c\u53ef\u89c6\u5316\u7684\u591a\u4e2a\u73af\u8282\u3002\u901a\u8fc7\u5b89\u88c5\u8fd9\u4e9b\u5305\uff0c\u7528\u6237\u53ef\u4ee5\u5feb\u901f\u83b7\u5f97\u5148\u8fdb\u7684\u5206\u6790\u5de5\u5177\uff0c\u8282\u7701\u7814\u7a76\u65f6\u95f4\uff0c\u964d\u4f4e\u5f00\u53d1\u6210\u672c\u3002\u638c\u63e1 R \u8bed\u8a00\u53ca\u5176\u5305\u7684\u5b89\u88c5\u4e0e\u4f7f\u7528\uff0c\u5bf9\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u7684\u65b0\u624b\u6765\u8bf4\uff0c\u610f\u5473\u7740\u53ef\u4ee5\u5229\u7528\u73b0\u6709\u7684\u8d44\u6e90\uff0c\u66f4\u6709\u6548\u5730\u8fdb\u884c\u6570\u636e\u5206\u6790\u4e0e\u89e3\u8bfb\u3002\u968f\u7740\u7814\u7a76\u7684\u6df1\u5165\uff0c\u7528\u6237\u5c06\u80fd\u591f\u6839\u636e\u81ea\u8eab\u9700\u6c42\u9009\u62e9\u5408\u9002\u7684\u5305\uff0c\u4ece\u800c\u63d0\u5347\u79d1\u7814\u7684\u6548\u7387\u548c\u8d28\u91cf\u3002<strong>\u6b22\u8fce\u5927\u5bb6\u79df\u8d41\u6211\u4eec\u7684\u670d\u52a1\u5668\uff01\u6211\u4eec\u4e0d\u4ec5\u63d0\u4f9b\u9ad8\u6027\u80fd\u7684\u4e91\u670d\u52a1\u5668\u6765\u6ee1\u8db3\u60a8\u7684\u9700\u6c42\uff0c\u8fd8\u63d0\u4f9b\u4e13\u4e1a\u7684\u6280\u672f\u652f\u6301\uff0c\u5e2e\u52a9\u60a8\u8f7b\u677e\u5b8c\u6210 R \u8bed\u8a00\u73af\u5883\u7684\u90e8\u7f72\u4e0e\u914d\u7f6e\u3002\u5982\u679c\u60a8\u6b63\u5728\u8fdb\u884c\u751f\u7269\u4fe1\u606f\u5b66\u3001\u7edf\u8ba1\u5206\u6790\u6216\u6570\u636e\u79d1\u5b66\u7b49\u7814\u7a76\uff0c\u5b89\u88c5 R \u5305\u662f\u60a8\u5de5\u4f5c\u7684\u91cd\u8981\u73af\u8282\u3002\u6211\u4eec\u53ef\u4ee5\u4e3a\u60a8\u63d0\u4f9b\u5feb\u901f\u3001\u7b80\u4fbf\u7684 R \u5305\u5b89\u88c5\u6307\u5bfc\uff0c\u786e\u4fdd\u60a8\u80fd\u591f\u987a\u5229\u4f7f\u7528\u5404\u79cd\u5f3a\u5927\u7684\u5de5\u5177\u548c\u8d44\u6e90\uff0c\u63d0\u5347\u60a8\u7684\u79d1\u7814\u6548\u7387\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u51e0\u79cd\u5728 R \u4e2d\u5b89\u88c5\u5305\u7684\u5e38\u89c1\u65b9\u6cd5\uff0c\u4e0b\u9762\u662f\u6bcf\u79cd\u65b9\u6cd5\u7684\u8be6\u7ec6\u8bf4\u660e\uff1a<\/p>\n\n\n\n<ol type=\"1\">\n<li><strong>CRAN \u4ed3\u5e93\u76f4\u63a5\u5b89\u88c5<\/strong>\uff1a<ol><li>\u4f7f\u7528 R \u7684 install.packages()&nbsp;\u51fd\u6570\u53ef\u4ee5\u76f4\u63a5\u4ece CRAN \u4ed3\u5e93\u5b89\u88c5\u5305\u3002\u793a\u4f8b\u4ee3\u7801\u5982\u4e0b\uff1a<\/li><\/ol>\n<ol>\n<li>install.packages(&#8220;\u5305\u540d&#8221;)<\/li>\n<\/ol>\n<\/li>\n<\/ol>\n\n\n\n<p>\u793a\u4f8b: install.packages(&#8220;remotes&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"560\" height=\"388\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732004983862_B7816A59-6344-4d6c-A918-1F999B775369.png?resize=560%2C388\" alt=\"\" class=\"wp-image-61783\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732004983862_B7816A59-6344-4d6c-A918-1F999B775369.png?w=560 560w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732004983862_B7816A59-6344-4d6c-A918-1F999B775369.png?resize=300%2C208 300w\" sizes=\"(max-width: 560px) 100vw, 560px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u9996\u6b21\u5b89\u88c5\u53ef\u80fd\u4f1a\u63d0\u793a\u5982\u4e0b \u8f93\u5165yes\u5373\u53ef<\/p>\n\n\n\n<p>&gt;&nbsp;install.packages<strong>(<\/strong>&#8220;remotes&#8221;<strong>)<\/strong><br>Warning&nbsp;in install.packages<strong>(<\/strong>&#8220;remotes&#8221;<strong>)<\/strong>&nbsp;:<br>&nbsp;&nbsp;&#8216;lib = &#8220;\/opt\/R\/4.4.1\/lib\/R\/library&#8221;&#8216;&nbsp;is not writable<br>Would&nbsp;you like to use a personal library instead?&nbsp;<strong>(<\/strong>yes\/No\/cancel<strong>)<\/strong>&nbsp;yes<br>Would&nbsp;you like to create a personal library<br>\u2018\/media\/desk16\/username\/R\/x86_64-pc-linux-gnu-library\/4.4\u2019<br>to&nbsp;install packages into?&nbsp;<strong>(<\/strong>yes\/No\/cancel<strong>)<\/strong>&nbsp;yes<\/p>\n\n\n\n<p>\u800c\u540e\u5f39\u51fa\u955c\u50cf\u9009\u62e9(\u5982\u679c\u670d\u52a1\u5668\u8bbe\u7f6e\u4e86\u5168\u5c40\u4ee3\u7406 \u5219\u4e0d\u5f39\u51fa) \u4e00\u822c\u9009\u62e9china\u4e0b\u9762\u4efb\u610f\u5e8f\u53f7\u5373\u53ef \u5982: 15<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"560\" height=\"160\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732004995804_CB9A88FD-577B-461f-83C6-2867B3B562E0.png?resize=560%2C160\" alt=\"\" class=\"wp-image-61784\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732004995804_CB9A88FD-577B-461f-83C6-2867B3B562E0.png?w=560 560w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732004995804_CB9A88FD-577B-461f-83C6-2867B3B562E0.png?resize=300%2C86 300w\" sizes=\"(max-width: 560px) 100vw, 560px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u7ed3\u679c\u6b63\u5e38\u8f93\u51fa\u4e3a* DONE (remotes) \u5c31\u662f\u5b89\u88c5\u6210\u529f\u4e86<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"560\" height=\"581\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005007825_9D1D3CC4-92CD-4756-AACE-BB5BAFC81CE2.png?resize=560%2C581\" alt=\"\" class=\"wp-image-61785\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005007825_9D1D3CC4-92CD-4756-AACE-BB5BAFC81CE2.png?w=560 560w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005007825_9D1D3CC4-92CD-4756-AACE-BB5BAFC81CE2.png?resize=289%2C300 289w\" sizes=\"(max-width: 560px) 100vw, 560px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<ul>\n<li><strong>\u5305\u4f4d\u7f6e\u5b89\u88c5<\/strong>\uff1a<ul><li>\u5982\u679c\u4f60\u6709\u5305\u7684\u538b\u7f29\u6587\u4ef6\uff0c\u53ef\u4ee5\u6307\u5b9a\u8be5\u6587\u4ef6\u7684\u4f4d\u7f6e\u8fdb\u884c\u5b89\u88c5\u3002\u4f7f\u7528 repos = NULL&nbsp;\u8868\u793a\u4e0d\u4ece CRAN \u4ed3\u5e93\u83b7\u53d6\uff0ctype = &#8220;source&#8221;&nbsp;\u8868\u793a\u4ee5\u6e90\u4ee3\u7801\u5f62\u5f0f\u5b89\u88c5\u3002\u793a\u4f8b\u4ee3\u7801\u5982\u4e0b\uff1a<\/li><\/ul><ul><li>install.packages(&#8220;\u5305\u4f4d\u7f6e&#8221;, repos =&nbsp;NULL, type =&nbsp;&#8220;source&#8221;)<\/li><\/ul><ul><li>\u4e00\u822c\u7528\u6765\u5904\u7406BiocManager\u5b89\u88c5\u63d0\u793a\u5347\u7ea7\u4e00\u5927\u5806\u5185\u5bb9<\/li><\/ul><ul><li><strong>\u4e3e\u4e2a\u4f8b\u5b50:<\/strong>&nbsp;<\/li><\/ul>\n<ul>\n<li>BiocManager::install(&#8220;celldex&#8221;)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"560\" height=\"530\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005020789_384C2F9C-7E21-491f-AFA0-BC0BD3EDC51D.png?resize=560%2C530\" alt=\"\" class=\"wp-image-61786\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005020789_384C2F9C-7E21-491f-AFA0-BC0BD3EDC51D.png?w=560 560w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005020789_384C2F9C-7E21-491f-AFA0-BC0BD3EDC51D.png?resize=300%2C284 300w\" sizes=\"(max-width: 560px) 100vw, 560px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<ul>\n<li>\u9996\u5148\u662f\u6700\u8ba8\u538c\u7684\u9519\u8bef\u4e4b\u4e00, \u5e38\u89c1\u5728\u5171\u4eab\u670d\u52a1\u5668\u4e0a, \u4f1a\u51fa\u73b0\u8def\u5f84\u9519\u8bef, \u53cd\u590d\u8c03\u6574\u90fd\u65e0\u6cd5\u5b89\u88c5, \u5e76\u4e14\u8fd9\u4e00\u4e0b\u5b50\u4e22\u4e86\u767e\u6765\u4e2a\u5305\u5347\u7ea7, \u4e00\u4e2a\u4e00\u4e2a\u9009\u5929\u90fd\u9ed1\u4e86, \u6211\u7684\u5efa\u8bae\u662f\u76f4\u63a5\u7565\u8fc7\u8fd9\u4e2a\u65b9\u5f0f\u3002<ul><li>\u5b9e\u9645\u63a8\u8350\u7684\u65b9\u5f0f\u662f\u91c7\u7528install.packages(&#8220;\u5305\u4f4d\u7f6e&#8221;, repos = NULL, type = &#8220;source&#8221;)\u65b9\u5f0f\u5b89\u88c5 , \u9996\u5148\u5c06celldex_1.14.0.tar.gz\u5305\u4e0b\u8f7d\u5230\u672c\u5730\u540e\u4e0a\u4f20\u670d\u52a1\u5668\u6216\u8005\u76f4\u63a5\u5728\u670d\u52a1\u5668\u4e0a\u4e0b\u8f7d\u597d, \u7136\u540e\u8fdb\u5165R\u4e2d\u5b89\u88c5<\/li><\/ul>\n<ul>\n<li>install.packages(&#8220;celldex_1.14.0.tar.gz&#8221;, repos = NULL, type = &#8220;source&#8221;)&nbsp;<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Bioconductor \u7ba1\u7406\u5668\u5b89\u88c5<\/strong>\uff1a<ul><li>\u5bf9\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u76f8\u5173\u7684\u5305\uff0c\u53ef\u4ee5\u4f7f\u7528 Bioconductor \u7684\u5305\u7ba1\u7406\u5668 BiocManager&nbsp;\u8fdb\u884c\u5b89\u88c5\u3002\u793a\u4f8b\u4ee3\u7801\u5982\u4e0b\uff1a(\u4e00\u822c\u4e0d\u63a8\u8350\u8fd9\u79cd\u65b9\u5f0f, \u5347\u7ea7\u4e00\u5927\u5806\u5305, \u5f71\u54cd\u4e4b\u524d\u7684\u4f9d\u8d56)<\/li><\/ul>\n<ul>\n<li>BiocManager::install(&#8220;\u5305\u540d&#8221;)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>\u4e0b\u8f7d\u5230R\u5305\u7684\u6e90\u7801\u4e4b\u540e\u7f16\u8bd1\u5b89\u88c5<\/strong>\uff1a<ul><li>\u6bd4\u5982\u4f7f\u7528 git clone&nbsp;\u83b7\u53d6\u7684\u5305\uff0c\u5982test01\u5305\u3002\u793a\u4f8b\u4ee3\u7801\u5982\u4e0b\uff1a<\/li><\/ul><ul><li>\u5728test01\u6587\u4ef6\u5939\u4e2d, \u4f7f\u7528\u4e0b\u9762\u4ee3\u7801\u8fdb\u884c\u7f16\u8bd1\u5b89\u88c5<\/li><\/ul>\n<ul>\n<li>install.packages(&#8220;.&#8221;, repos =&nbsp;NULL, type =&nbsp;&#8220;source&#8221;)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>devtools\u5b89\u88c5<\/strong>\n<ul>\n<li>\u4e3e\u4e2a\u4f8b\u5b50 : devtools::install_github(&#8220;jinworks\/CellChat&#8221;)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"560\" height=\"213\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005030188_F31666BC-1471-4421-9625-3133D4E4985E.png?resize=560%2C213\" alt=\"\" class=\"wp-image-61787\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005030188_F31666BC-1471-4421-9625-3133D4E4985E.png?w=560 560w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005030188_F31666BC-1471-4421-9625-3133D4E4985E.png?resize=300%2C114 300w\" sizes=\"(max-width: 560px) 100vw, 560px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u4e0a\u56fe\u7684\u63d0\u793a\u53ef\u4ee5\u76f4\u63a5\u56de\u8f66\u5ffd\u7565, \u53ea\u662f\u5efa\u8bae\u66f4\u65b0, \u800c\u5728Bioconductor\u4e2d\u5219\u662f\u5f3a\u5236\u66f4\u65b0\u3002<\/p>\n\n\n\n<p>\u7f16\u8bd1\u5b89\u88c5\u5b8c\u6210\u540e \u4e5f\u4f1a\u51fa\u73b0\u7ecf\u5178\u63d0\u793a&nbsp;* DONE (CellChat)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"560\" height=\"284\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005039157_8A2898DF-56E8-48d2-A75B-4A6BE89E2C0B.png?resize=560%2C284\" alt=\"\" class=\"wp-image-61788\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005039157_8A2898DF-56E8-48d2-A75B-4A6BE89E2C0B.png?w=560 560w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005039157_8A2898DF-56E8-48d2-A75B-4A6BE89E2C0B.png?resize=300%2C152 300w\" sizes=\"(max-width: 560px) 100vw, 560px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u901a\u8fc7\u4ee5\u4e0a\u6b65\u9aa4\uff0c\u60a8\u5e94\u8be5\u80fd\u591f\u6210\u529f\u5b89\u88c5\u548c\u914d\u7f6e R \u5305\uff0c\u8fd9\u4e3a\u60a8\u5728\u751f\u7269\u4fe1\u606f\u5b66\u548c\u6570\u636e\u5206\u6790\u9886\u57df\u63d0\u4f9b\u4e86\u5f3a\u5927\u7684\u652f\u6301\u3002R 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