{"id":37096,"date":"2025-05-14T07:11:30","date_gmt":"2025-05-13T23:11:30","guid":{"rendered":"https:\/\/www.wsisp.com\/helps\/37096.html"},"modified":"2025-05-14T07:11:30","modified_gmt":"2025-05-13T23:11:30","slug":"%e6%80%8e%e4%b9%88%e4%bd%bf%e7%94%a8%e6%9c%8d%e5%8a%a1%e5%99%a8%e8%bf%90%e8%a1%8cpyscenic","status":"publish","type":"post","link":"https:\/\/www.wsisp.com\/helps\/37096.html","title":{"rendered":"\u600e\u4e48\u4f7f\u7528\u670d\u52a1\u5668\u8fd0\u884cpySCENIC"},"content":{"rendered":"<h2>\u524d\u8a00<\/h2>\n<p>\u2003\u2003\u6211\u4eec\u6ce8\u610f\u5230\u5728\u5176\u4ed6\u7684\u4e00\u4e9b\u8bba\u575b&#xff0c;\u6709\u4e00\u4e9b\u7528\u6237\u53cd\u9988&#xff0c;\u5728\u670d\u52a1\u5668\u4e0a\u9762\u8fd0\u884cpyscenic\u4e0d\u592a\u987a\u7545\u3002\u672c\u6587\u6211\u4eec\u6574\u7406\u4e86\u5728\u670d\u52a1\u5668\u4e0a\u8fd0\u884cpyscenic\u7684\u4e09\u4e2a\u65b9\u6cd5\u4f9b\u5927\u5bb6\u53c2\u8003&#xff0c;\u5206\u522b\u662fconda\u5b89\u88c5pyscenic\u8fd0\u884c\u3001arboreto_with_multiprocessing\u8fd0\u884c\u3001\u5bb9\u5668\u5316\u8fd0\u884c\u3002\u603b\u7684\u6765\u8bf4&#xff0c;\u63a8\u8350\u4f7f\u7528\u5bb9\u5668\u5316\u65b9\u5f0f\u8fd0\u884c&#xff0c;\u5176\u6b21\u662farboreto_with_multiprocessing\u65b9\u5f0f&#xff0c;\u6700\u6b21\u662fconda\u5b89\u88c5pyscenic\u8fd0\u884c\u7684\u65b9\u5f0f\u3002<\/p>\n<p>\u2003\u2003pyscenic\u7684\u4e09\u4e2a\u6b65\u9aa4&#xff0c;grn\u3001ctx\u3001aucell&#xff0c;\u5206\u522b\u8017\u65f6\u7684\u7ea7\u522b\u662f\u5341\u51e0\u4e2a\u5c0f\u65f6\u3001\u4e24\u4e09\u4e2a\u5c0f\u65f6\u3001\u534a\u5c0f\u65f6&#xff0c;\u8fd0\u884c\u65f6\u95f4\u4f9d\u636e\u5b9e\u9645\u4f7f\u7528\u6570\u636e\u5927\u5c0f\u3001\u670d\u52a1\u5668\u8d1f\u8f7d\u7b49\u5177\u4f53\u60c5\u51b5\u6709\u4e0d\u540c\u7684\u65f6\u95f4\u8868\u73b0&#xff0c;\u4ee5\u4e0a\u65f6\u95f4\u4ec5\u4f9b\u53c2\u8003&#xff0c;\u603b\u4e4b\u4e09\u90e8\u66f2\u8017\u65f6\u662f\u8d8a\u6765\u8d8a\u77ed\u7684\u3002<\/p>\n<ul>\n<li>\u4e00\u4e9b\u4f18\u8d28\u7684\u6587\u6863\n<li>\u300a\u4f7f\u7528\u897f\u67da\u4e91\u81ea\u5b66pySCENIC\u6240\u9047Error\u300b<\/li>\n<li>\u300a\u4f7f\u7528pyscenic\u505a\u8f6c\u5f55\u56e0\u5b50\u5206\u6790\u300b<\/li>\n<li>\u300apySCENIC\u62a5\u9519\u3001\u89e3\u51b3\u548c\u5b8c\u6574\u6d41\u7a0b(IOS\u7cfb\u7edf)\u300b<\/li>\n<li>\u300aPyScenic\u6559\u5b66&#xff08;\u5bb9\u5668\u5316&#xff09;\u300b<\/li>\n<\/li>\n<\/ul>\n<h2>conda\u5b89\u88c5pyscenic\u8fd0\u884c<\/h2>\n<h3>Dask<\/h3>\n<ul>\n<li>\u9ed8\u8ba4\u7684pyscenic\u662f\u4f7f\u7528\u5230\u4e86Dask\u7684&#xff0c;Dask\u662f\u4e00\u4e2apython\u7f16\u5199\u7684&#xff0c;\u7075\u6d3b\u7684\u5927\u6570\u636e\u5e76\u884c\u8ba1\u7b97\u5e93(\u6846\u67b6)&#xff0c;\u80fd\u5728\u5206\u5e03\u5f0f\u96c6\u7fa4\u4e2d\u8fdb\u884c\u5206\u5e03\u5f0f\u5e76\u884c\u8ba1\u7b97&#xff0c;\u4e5f\u53ef\u4ee5\u5728\u5355\u673a&#xff08;\u591a\u6838\u5fc3&#xff09;\u4e2d\u8fdb\u884c\u4f2a\u5206\u5e03\u5f0f\u5e76\u884c\u8ba1\u7b97\u3002<\/li>\n<\/ul>\n<h3>\u73af\u5883\u914d\u7f6e\u4e0e\u8fd0\u884c<\/h3>\n<ul>\n<li>\u53c2\u8003\u8bba\u575b\u91cc\u67d0\u4f4d\u5927\u4f6c\u7684\u8bc4\u8bba&#xff0c;pyscenic\u5b58\u5728\u4e00\u4e9b\u7248\u672c\u7684\u95ee\u9898&#xff0c;\u6545\u5b89\u88c5\u7684\u65f6\u5019\u9700\u8981\u8fdb\u884c\u4e00\u4e9b\u964d\u7ea7\u5904\u7406\u3002<\/li>\n<\/ul>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231126-6823d19e4245c.png\" alt=\"\" \/><\/p>\n<p>mamba create -y -n pyscenic310 python&#061;3.10 -vv<\/p>\n<p>mamba activate pyscenic310<\/p>\n<p>pip config set global.index-url http:\/\/mirror.xiyoucloud.pro:63333\/repository\/pypi\/simple<br \/>\npip config set install.trusted-host mirror.xiyoucloud.pro<br \/>\npip config set global.timeout 6000<\/p>\n<p># pip \u4ece git \u6e90\u7801\u4ed3\u5e93\u76f4\u63a5 install \u3002\u8981\u6c42\u662f\u8fd9\u4e2agithub\u4ed3\u5e93\u5185\u8981\u6709setup.py\u6587\u4ef6\u3002\u3010\u8fd9\u91cc\u6709\u53ef\u80fd\u9700\u8981\u9b54\u6cd5\u3011<br \/>\npip install git&#043;https:\/\/github.com\/aertslab\/pySCENIC<\/p>\n<p>pip install numpy&#061;&#061;1.23.5<br \/>\npip install distributed&#061;&#061;2024.2.1<br \/>\npip install dask-expr&#061;&#061;0.5.3<br \/>\npip install numba&#061;&#061;0.56.4<\/p>\n<p># \u7b2c\u4e00\u6b65 grn&#xff0c;sample.loom\u3001hs_hgnc_tfs.txt\u662f\u8f93\u5165&#xff0c;\u4ea7\u51fa\u662fadj.sample.tsv<br \/>\ntime pyscenic grn &#8211;num_workers 20 &#8211;output adj.sample.tsv &#8211;method grnboost2 sample.loom hs_hgnc_tfs.txt<\/p>\n<p># \u7b2c\u4e8c\u6b65 ctx \u8f93\u5165\u662fhg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather\u3001motifs-v9-nr.hgnc-m0.001-o0.0.tbl&#xff0c;\u8f93\u51fa\u662freg.csv<br \/>\ntime pyscenic ctx adj.sample.tsv hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather &#8211;annotations_fname motifs-v9-nr.hgnc-m0.001-o0.0.tbl &#8211;expression_mtx_fname sample.loom &#8211;mode &#034;dask_multiprocessing&#034; &#8211;output reg.csv &#8211;num_workers 10 &#8211;mask_dropouts<\/p>\n<p># \u7b2c\u4e09\u6b65 aucell&#xff0c;sample.loom\u3001reg.csv\u662f\u8f93\u5165&#xff0c;\u4ea7\u51fa\u662fsample_SCENIC.loom<br \/>\ntime pyscenic aucell sample.loom reg.csv &#8211;output sample_SCENIC.loom &#8211;num_workers 10<\/p>\n<h3>UserWarning: Port 8787 is already in use\u95ee\u9898<\/h3>\n<ul>\n<li>Dask\u96c6\u7fa4\u542f\u52a8\u7684\u65f6\u5019&#xff0c;\u4f1a\u542f\u52a8\u4e00\u4e2aweb\u670d\u52a1&#xff08;web\u670d\u52a1\u7684\u53ef\u89c6\u5316\u754c\u9762\u5927\u6982\u957f\u4e0b\u56fe\u8fd9\u6837&#xff0c;\u53ef\u4ee5\u770b\u5230\u8ba1\u7b97\u4efb\u52a1\u7684\u8d44\u6e90\u4f7f\u7528\u60c5\u51b5\u4ee5\u53ca\u4efb\u52a1\u62d3\u6251\u56fe&#xff09;\u5bf9\u96c6\u7fa4\u7684\u8fd0\u884c\u8fdb\u884c\u6570\u636e\u7684\u53ef\u89c6\u5316&#xff0c;\u8be5\u670d\u52a1\u76d1\u542c8787\u7aef\u53e3&#xff0c;\u800cRstudio\u4e5f\u662f\u76d1\u542c8787\u7aef\u53e3&#xff0c;\u4e8c\u8005\u5c31\u51b2\u7a81\u4e86&#xff0c;\u4f46\u662f\u8fd9\u4e2a\u4e0d\u5f71\u54cd\u5b9e\u9645\u8fd0\u884c&#xff0c;\u56e0\u4e3aDask\u4f1a\u968f\u673a\u9009\u62e9\u4e00\u4e2a\u672a\u4f7f\u7528\u7684\u7aef\u53e3\u6765\u8fd0\u884c\u7684\u3002<\/li>\n<\/ul>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231126-6823d19e5715c.png\" alt=\"\" \/><\/p>\n<h3>Distributed core Error&#xff0c; Cancelled Error&#xff0c;CommClosedError\u95ee\u9898<\/h3>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231126-6823d19e955e4.png\" alt=\"\" \/><\/p>\n<ul>\n<li>\u8fd9\u79cd\u62a5\u9519\u4e3aDask\u7684\u5206\u5e03\u5f0f\u8fd0\u7b97\u534f\u8c03\u5931\u8d25\u5bfc\u81f4\u8fd0\u884c\u62a5\u9519&#xff0c;\u6211\u4eec\u5355\u72ec\u8c03\u7528Dask\u5e93\u662f\u6ca1\u6709\u95ee\u9898\u7684&#xff0c;\u670d\u52a1\u7aef\u4e0e\u5ba2\u6237\u7aef\u90fd\u80fd\u6b63\u5e38\u542f\u52a8&#xff0c;\u4e5f\u80fd\u8c03\u7528\u591a\u4e2a\u6838\u5fc3\u8fdb\u884c\u5e76\u884c\u8ba1\u7b97\u3002\u95ee\u9898\u6709\u53ef\u80fd\u51fa\u5728pyscenic\u8c03\u7528Dask\u7684\u65f6\u5019&#xff0c;\u6709\u4ec0\u4e48\u5730\u65b9\u6ca1\u5904\u7406\u597d&#xff0c;\u5bfc\u81f4\u8fdb\u884c\u591a\u7ebf\u7a0b\u8fd0\u7b97\u7684\u65f6\u5019\u5076\u5c14\u51fa\u9519&#xff0c;\u4e0b\u9762\u7ed9\u51fa\u9a8c\u8bc1\u5728\u897f\u67da\u4e91\u670d\u52a1\u5668\u8fd0\u884cDask\u662f\u5426\u6709\u95ee\u9898\u7684Demo&#xff0c;\u4e0epyscenic\u6ca1\u6709\u4ec0\u4e48\u5173\u7cfb&#xff0c;\u5927\u5bb6\u770b\u770b\u5373\u53ef\u3002<\/li>\n<\/ul>\n<p>from dask.distributed import LocalCluster, Client<\/p>\n<p># \u521b\u5efa\u4e00\u4e2a\u672c\u5730\u7684\u4f2a\u5206\u5e03\u5f0f\u96c6\u7fa4&#xff0c;\u76d1\u542c14951\u7aef\u53e3&#xff0c;\u8fd9\u6837\u5c31\u4e0d\u4f1a\u4e0eRstudio\u76848787\u7aef\u53e3\u51b2\u7a81\u4e86<br \/>\ncluster &#061; LocalCluster(scheduler_port&#061;14950,dashboard_address&#061;&#034;:14951&#034;)<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231127-6823d19f000a2.png\" alt=\"\" \/><\/p>\n<p>from dask.distributed import Client<\/p>\n<p># \u521b\u5efaDask\u96c6\u7fa4\u5ba2\u6237\u7aef<br \/>\nclient &#061; Client(&#034;127.0.0.1:14950&#034;)<\/p>\n<p># \u4f7f\u7528Dask\u8fdb\u884c\u5e76\u884c\u8ba1\u7b97<br \/>\nimport dask.array as da<br \/>\nimport numpy as np<\/p>\n<p># \u521b\u5efa\u4e00\u4e2a\u5927\u6570\u7ec4<br \/>\nx &#061; da.from_array(np.random.random((10000, 10000)), chunks&#061;(1000, 1000))<\/p>\n<p># \u5e76\u884c\u8ba1\u7b97\u6570\u7ec4\u7684\u5e73\u5747\u503c<br \/>\nmean &#061; x.mean().compute()<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231127-6823d19f26a1e.png\" alt=\"\" \/><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231127-6823d19f3df8c.png\" alt=\"\" \/><\/p>\n<h2>arboreto_with_multiprocessing\u8fd0\u884c<\/h2>\n<ul>\n<li>\n<p>\u5982\u679c\u662f\u5355\u673a\u8fd0\u884cpyscenic&#xff0c;\u8fd8\u53ef\u4ee5\u4f7f\u7528arboreto_with_multiprocessing\u6765\u8fd0\u884c\u3002 arboreto_with_multiprocessing.py\u6587\u4ef6\u5728\u5b89\u88c5\u4e86pyscenic\u540e\u5c31\u80fd\u76f4\u63a5\u4f7f\u7528\u4e86\u7684&#xff0c;\u5176\u7279\u522b\u9002\u5408\u5355\u673a\u8fd0\u884c\u7684\u60c5\u51b5&#xff0c;\u56e0\u4e3a\u4e0d\u4f7f\u7528Dask&#xff0c;\u653e\u5f03\u4e86\u591a\u670d\u52a1\u5668\u8282\u70b9\u8fd0\u884c\u7684\u80fd\u529b&#xff0c;\u4f46\u662f\u597d\u5904\u662f\u4f9d\u8d56\u66f4\u5c11&#xff0c;\u66f4\u52a0\u7a33\u5b9a&#xff0c;\u53ef\u4ee5\u907f\u514d\u51fa\u73b0\u4e0a\u9762\u8bf4\u7684Dask\u5206\u5e03\u5f0f\u8fd0\u7b97\u534f\u8c03\u5931\u8d25\u5bfc\u81f4\u8fd0\u884c\u62a5\u9519\u3002<\/p>\n<\/li>\n<li>\n<p>Arboreto\u662fpyscenic\u7684\u4e00\u4e2a\u4f9d\u8d56\u5e93&#xff0c;\u4e3b\u8981\u7528\u4e8e\u52a0\u901fGRN\u63a8\u65ad&#xff0c;\u7279\u522b\u662f\u4f7f\u7528\u591a\u8fdb\u7a0b\u6765\u5e76\u884c\u5316GENIE3\u6216GRNBoost2\u7b97\u6cd5\u3002\u6240\u4ee5arboreto_with_multiprocessing.py\u5e94\u8be5\u53ea\u8d1f\u8d23\u7b2c\u4e00\u6b65\u7684\u5171\u8868\u8fbe\u7f51\u7edc\u63a8\u65ad&#xff0c;\u7b2c\u4e8c\u3001\u7b2c\u4e09\u6b65\u548c\u65b9\u6cd5\u4e00\u662f\u4e00\u6837\u7684\u3002<\/p>\n<\/li>\n<\/ul>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231127-6823d19f615ba.png\" alt=\"\" \/><\/p>\n<h3>\u73af\u5883\u914d\u7f6e\u4e0e\u8fd0\u884c<\/h3>\n<p>mamba create -y -n pyscenic379-arboreto python&#061;3.7.9 -vv<\/p>\n<p>mamba activate pyscenic379-arboreto<\/p>\n<p>mamba install -y numpy&#061;&#061;1.19.5 -vv<\/p>\n<p>pip install pyscenic&#061;&#061;0.12.0<\/p>\n<p># \u7b2c\u4e00\u6b65<br \/>\ntime arboreto_with_multiprocessing.py &#8211;num_workers 20 &#8211;output adj.sample.tsv &#8211;method grnboost2 sample.loom hs_hgnc_tfs.txt<\/p>\n<p># \u7b2c\u4e8c\u6b65<br \/>\ntime pyscenic ctx adj.sample.tsv hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather &#8211;annotations_fname motifs-v9-nr.hgnc-m0.001-o0.0.tbl &#8211;expression_mtx_fname sample.loom &#8211;mode &#034;dask_multiprocessing&#034; &#8211;output reg.csv &#8211;num_workers 10 &#8211;mask_dropouts<\/p>\n<p># \u7b2c\u4e09\u6b65<br \/>\ntime pyscenic aucell sample.loom reg.csv &#8211;output sample_SCENIC.loom &#8211;num_workers 10<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231127-6823d19fabf17.png\" alt=\"\" \/><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231127-6823d19fce8f2.png\" alt=\"\" \/><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231128-6823d1a013859.png\" alt=\"\" \/><\/p>\n<h3>\u7a0b\u5e8f\u6ca1\u6709\u4f7f\u7528\u591a\u6838\u5fc3\u95ee\u9898<\/h3>\n<ul>\n<li>\u6b64\u95ee\u9898\u5728\u4ed3\u5e93\u7684issue&#xff08;https:\/\/github.com\/aertslab\/pySCENIC\/issues\/463&#xff09;\u4e2d\u6709\u63d0\u5230&#xff0c;\u660e\u660e\u8bbe\u7f6e\u4e86num_workers\u4e3a20&#xff0c;\u4f46\u662f\u5b9e\u9645\u53ea\u6709\u5355\u6838\u5fc3\u5728\u8fd0\u884c\u3002\u6709\u7528\u6237\u7ed9\u51fa\u4e86\u89e3\u51b3\u65b9\u6848\u662f\u5c06pyscenic\u964d\u7ea7\u52300.12.0\u7248\u672c&#xff0c;\u5b9e\u6d4b\u53ef\u884c\u3002\u540c\u65f6\u5b98\u65b9\u4e5f\u6307\u51fa\u4e86&#xff0c;\u53ef\u4ee5\u4f7f\u7528\u5bb9\u5668\u5316\u8fd0\u884c\u3002<\/li>\n<\/ul>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231128-6823d1a050a8e.png\" alt=\"\" \/><\/p>\n<h2>\u5bb9\u5668\u5316\u8fd0\u884c<\/h2>\n<ul>\n<li>\u53ef\u4ee5\u770b\u5230&#xff0c;\u524d\u9762\u4e24\u4e2a\u65b9\u6cd5\u90fd\u9700\u8981\u5b89\u88c5\u7279\u5b9a\u7248\u672c\u7684\u4f9d\u8d56\u624d\u80fd\u8fd0\u884c&#xff0c;\u6bd4\u8f83\u590d\u6742\u3002\u4f7f\u7528\u5bb9\u5668\u5316\u6280\u672f&#xff0c;\u53ef\u4ee5\u5c06\u4e00\u6574\u5957\u6253\u5305\u597d\u7684\u8f6f\u4ef6\u62c9\u53d6\u4e0b\u6765\u8fd0\u884c&#xff0c;\u514d\u53bb\u4e86\u5f88\u591a\u73af\u5883\u914d\u7f6e\u8c03\u8bd5\u7684\u70e6\u607c\u3002<\/li>\n<\/ul>\n<h3>pyscenic\u7684\u53ef\u7528\u7248\u672c<\/h3>\n<ul>\n<li>pip<\/li>\n<\/ul>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231128-6823d1a0ab5b7.png\" alt=\"\" \/><\/p>\n<ul>\n<li>docker<\/li>\n<\/ul>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231129-6823d1a1060d9.png\" alt=\"\" \/><\/p>\n<h3>\u73af\u5883\u914d\u7f6e\u4e0e\u8fd0\u884c<\/h3>\n<ul>\n<li>pyscenic\u7684\u6700\u65b0\u7248\u672c\u4e3a0.12.1&#xff0c;\u7ef4\u62a4\u65f6\u95f4\u662f2\u5e74\u524d&#xff0c;\u6700\u8fd1\u7684\u51e0\u4e2a\u7248\u672c\u5206\u522b\u662f&#xff1a;0.12.1\u30010.12.0\u30010.11.2\u30010.11.1\u3002<\/li>\n<li>\u7531\u4e8e\u56fd\u5185\u7f51\u7edc\u95ee\u9898&#xff0c;\u6240\u4ee5\u9700\u8981\u4ece\u897f\u67da\u4e91\u7684docker\u4ed3\u5e93&#xff08;\u62c9\u53d6\u4e4b\u524d\u9700\u8981\u8fdb\u884cdocker\u4ed3\u5e93\u7684\u914d\u7f6e&#xff0c;\u5177\u4f53\u4ed3\u5e93\u7528\u6cd5&#xff1a;\u897f\u67da\u4ed3\u5e93\u96c6\u5408&#xff09;\u4e2d\u62c9\u53d6\u5bf9\u5e94\u7684\u955c\u50cf&#xff0c;\u5426\u5219\u4f1a\u51fa\u73b0\u62c9\u53d6\u955c\u50cf\u8d85\u65f6\u62a5\u9519\u7684\u60c5\u51b5\u3002<\/li>\n<\/ul>\n<p>sudo docker pull mirror.xiyoucloud.pro:63331\/aertslab\/pyscenic:0.12.1 <\/p>\n<p>sudo docker tag mirror.xiyoucloud.pro:63331\/aertslab\/pyscenic:0.12.1 aertslab\/pyscenic:0.12.1<\/p>\n<p># \u7b2c\u4e00\u6b65<br \/>\ntime docker run -it &#8211;rm -v ${HOME}\/pyscenic\/docker:\/data aertslab\/pyscenic:0.12.1 pyscenic grn &#8211;num_workers 20 -o \/data\/adj.sample.tsv &#8211;method grnboost2 \/data\/sample.loom \/data\/hs_hgnc_tfs.txt<\/p>\n<p># \u7b2c\u4e8c\u6b65<br \/>\ntime docker run -it &#8211;rm -v ${HOME}\/pyscenic\/docker:\/data aertslab\/pyscenic:0.12.1 pyscenic ctx \/data\/adj.sample.tsv \/data\/hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather &#8211;annotations_fname \/data\/motifs-v9-nr.hgnc-m0.001-o0.0.tbl &#8211;expression_mtx_fname \/data\/sample.loom &#8211;mode &#034;dask_multiprocessing&#034; &#8211;output \/data\/reg.csv &#8211;num_workers 10 &#8211;mask_dropouts<\/p>\n<p># \u7b2c\u4e09\u6b65<br \/>\ntime docker run -it &#8211;rm -v ${HOME}\/pyscenic\/docker:\/data aertslab\/pyscenic:0.12.1 pyscenic aucell \/data\/sample.loom \/data\/reg.csv &#8211;output \/data\/sample_SCENIC.loom &#8211;num_workers 10<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231129-6823d1a13af37.png\" alt=\"\" \/><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231129-6823d1a151883.png\" alt=\"\" \/><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231129-6823d1a16dc58.png\" alt=\"\" \/><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231129-6823d1a1a46d3.png\" alt=\"\" \/><\/p>\n<h2>\u7ed3\u8bed<\/h2>\n<p>\u2003\u2003\u5982\u679c\u9047\u5230\u5728\u897f\u67da\u4e91\u670d\u52a1\u5668\u8fd0\u884c\u8f6f\u4ef6\u6b7b\u6d3b\u8fd0\u884c\u4e0d\u6210\u529f&#xff0c;\u751a\u81f3\u8fde\u670b\u53cb\u4e5f\u8fd0\u884c\u4e0d\u6210\u529f&#xff0c;\u95ee\u9898\u51fa\u73b0\u201c\u7fa4\u4f53\u73b0\u8c61\u201d&#xff0c;\u8bf7\u53ca\u65f6\u8054\u7cfb\u6211\u4eec\u3002\u6211\u4eec\u4f1a\u5c3d\u6700\u5927\u53ef\u80fd\u4e3a\u60a8\u89e3\u51b3&#xff0c;\u5e76\u50cf\u6b64\u6587\u4e00\u6837\u603b\u7ed3\u51fa\u6765\u5e2e\u52a9\u5927\u5bb6\u3002\u5982\u679c\u76f8\u5173\u6280\u672f\u4eba\u5458\u5904\u7406\u4e0d\u529b&#xff0c;\u53ef\u76f4\u63a5\u8054\u7cfb\u6280\u672f\u603b\u8d1f\u8d23\u4eba\u5c0f\u67da\u5b50\u8fdb\u884c\u53cd\u9988\u6216\u6295\u8bc9&#xff0c;\u5c0f\u67da\u5b50\u5c06\u5c3d\u5feb\u4e3a\u5927\u5bb6\u534f\u8c03\u89e3\u51b3\u95ee\u9898\u3002<\/p>\n<hr \/>\n<p>\u2003\u2003\u5982\u679c\u5927\u5bb6\u5bf9\u6211\u4eec\u7684\u5185\u5bb9\u6709\u4efb\u4f55\u53cd\u9988&#xff0c;\u6216\u8005\u6709\u7279\u5b9a\u7684\u8f6f\u4ef6\u4f7f\u7528\u6559\u7a0b\u9700\u6c42&#xff0c;\u6b22\u8fce\u5728\u540e\u53f0\u7559\u8a00\u544a\u8bc9\u6211\u4eec&#xff0c;\u6211\u4eec\u7cfb\u7edf\u6574\u7406\u540e\u4e0e\u5927\u5bb6\u5206\u4eab\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u6587\u7ae0\u6d4f\u89c8\u9605\u8bfb1.3k\u6b21\uff0c\u70b9\u8d5e24\u6b21\uff0c\u6536\u85cf28\u6b21\u3002\u672c\u6587\u6211\u4eec\u6574\u7406\u4e86\u5728\u670d\u52a1\u5668\u4e0a\u8fd0\u884cpyscenic\u7684\u4e09\u4e2a\u65b9\u6cd5\u4f9b\u5927\u5bb6\u53c2\u8003\uff0c\u5206\u522b\u662fconda\u5b89\u88c5pyscenic\u8fd0\u884c\u3001arboreto_with_multiprocessing\u8fd0\u884c\u3001\u5bb9\u5668\u5316\u8fd0\u884c\u3002_pyscenic<\/p>\n","protected":false},"author":2,"featured_media":37079,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[58,3208,43,2299,3207,44],"topic":[],"class_list":["post-37096","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-server","tag-linux","tag-pyscenic","tag-43","tag-2299","tag-3207","tag-44"],"yoast_head":"<!-- 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content=\"\u6587\u7ae0\u6d4f\u89c8\u9605\u8bfb1.3k\u6b21\uff0c\u70b9\u8d5e24\u6b21\uff0c\u6536\u85cf28\u6b21\u3002\u672c\u6587\u6211\u4eec\u6574\u7406\u4e86\u5728\u670d\u52a1\u5668\u4e0a\u8fd0\u884cpyscenic\u7684\u4e09\u4e2a\u65b9\u6cd5\u4f9b\u5927\u5bb6\u53c2\u8003\uff0c\u5206\u522b\u662fconda\u5b89\u88c5pyscenic\u8fd0\u884c\u3001arboreto_with_multiprocessing\u8fd0\u884c\u3001\u5bb9\u5668\u5316\u8fd0\u884c\u3002_pyscenic\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.wsisp.com\/helps\/37096.html\" \/>\n<meta property=\"og:site_name\" content=\"\u7f51\u7855\u4e92\u8054\u5e2e\u52a9\u4e2d\u5fc3\" \/>\n<meta property=\"article:published_time\" content=\"2025-05-13T23:11:30+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2025\/05\/20250513231126-6823d19e4245c.png\" \/>\n<meta name=\"author\" content=\"admin\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" 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