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  145. <a href="/-dao-chu-SingleR-xu-yao-de-shu-ju" target="_self">
  146. <img src="https://api.limour.top/randomImg?d=2022-10-04 17:20:44" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】导出SingleR需要的数据">
  147. </a>
  148. </div>
  149. <article class="col-12 col-md-8 mx-auto index-info">
  150. <h2 class="index-header">
  151. <a href="/-dao-chu-SingleR-xu-yao-de-shu-ju" target="_self">
  152. 【迁移】导出SingleR需要的数据
  153. </a>
  154. </h2>
  155. <a class="index-excerpt " href="/-dao-chu-SingleR-xu-yao-de-shu-ju" target="_self">
  156. <div>
  157. loom文件使用记录 随着单细胞数据量的增长,计算要求成指数增长,当数据量大于10万个细胞的时候,seurat包分析就显得非常有压力了,因为在实时内存中储存数据就变得非常困难,HDF5数据格式提供了高效的磁盘存储,而不是在内存中存储数据,这就将分析扩展到大规模数据集,甚至可以达到大于100万细胞的级别 ,Linnarson实验室开发了一种基于hdf5的数据结构,loom,可以方便地存储单细胞基因组
  158. </div>
  159. </a>
  160. <div class="index-btm post-metas">
  161. <div class="post-meta mr-3">
  162. <i class="iconfont icon-date"></i>
  163. <time datetime="2022-10-04 17:20" pubdate>
  164. 2022-10-04
  165. </time>
  166. </div>
  167. <div class="post-meta">
  168. <i class="iconfont icon-tags"></i>
  169. <a href="/tags/singler/">#SingleR</a>
  170. </div>
  171. </div>
  172. </article>
  173. </div>
  174. <div class="row mx-auto index-card">
  175. <div class="col-12 col-md-4 m-auto index-img">
  176. <a href="/gei-VMware-xu-ni-ji-jia-ying-pan" target="_self">
  177. <img src="https://api.limour.top/randomImg?d=2022-10-02 17:55:18" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】给VMware虚拟机加硬盘">
  178. </a>
  179. </div>
  180. <article class="col-12 col-md-8 mx-auto index-info">
  181. <h2 class="index-header">
  182. <a href="/gei-VMware-xu-ni-ji-jia-ying-pan" target="_self">
  183. 【迁移】给VMware虚拟机加硬盘
  184. </a>
  185. </h2>
  186. <a class="index-excerpt " href="/gei-VMware-xu-ni-ji-jia-ying-pan" target="_self">
  187. <div>
  188. 买了一台零刻 SER5 Pro 32G作为虚拟机的宿主机,用了一个月感觉还行,准备加装一个铠侠TC10 1T SATA3固态。小心排线接口上有个黑色的东东,先用镊子挑起来再拔。然后虚拟机设置里添加磁盘。 挂载磁盘并设置开机自动mount sudo su fdisk -l #i查看可挂载磁盘 mkfs.ext4 /dev/sdb #格式化为ext4 # apt install util-linux
  189. </div>
  190. </a>
  191. <div class="index-btm post-metas">
  192. <div class="post-meta mr-3">
  193. <i class="iconfont icon-date"></i>
  194. <time datetime="2022-10-02 17:55" pubdate>
  195. 2022-10-02
  196. </time>
  197. </div>
  198. <div class="post-meta">
  199. <i class="iconfont icon-tags"></i>
  200. <a href="/tags/vmware/">#VMware</a>
  201. </div>
  202. </div>
  203. </article>
  204. </div>
  205. <div class="row mx-auto index-card">
  206. <div class="col-12 col-md-4 m-auto index-img">
  207. <a href="/ji-yu-NMF-fen-jie-de-jiang-wei-ju-lei" target="_self">
  208. <img src="https://api.limour.top/randomImg?d=2022-10-02 17:28:30" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】基于NMF分解的降维聚类">
  209. </a>
  210. </div>
  211. <article class="col-12 col-md-8 mx-auto index-info">
  212. <h2 class="index-header">
  213. <a href="/ji-yu-NMF-fen-jie-de-jiang-wei-ju-lei" target="_self">
  214. 【迁移】基于NMF分解的降维聚类
  215. </a>
  216. </h2>
  217. <a class="index-excerpt " href="/ji-yu-NMF-fen-jie-de-jiang-wei-ju-lei" target="_self">
  218. <div>
  219. 安装补充包 conda activate seurat conda install -c conda-forge r-nmf -y conda install -c conda-forge r-fastica -y 获取非负表达矩阵 使用《使用metacell进行分群聚类》中的数据 1234567891011121314151617sce &lt;- readRDS(&#x27;SRX8890
  220. </div>
  221. </a>
  222. <div class="index-btm post-metas">
  223. <div class="post-meta mr-3">
  224. <i class="iconfont icon-date"></i>
  225. <time datetime="2022-10-02 17:28" pubdate>
  226. 2022-10-02
  227. </time>
  228. </div>
  229. <div class="post-meta">
  230. <i class="iconfont icon-tags"></i>
  231. <a href="/tags/nmf/">#nmf</a>
  232. </div>
  233. </div>
  234. </article>
  235. </div>
  236. <div class="row mx-auto index-card">
  237. <div class="col-12 col-md-4 m-auto index-img">
  238. <a href="/shi-yong-metacell-jin-hang-fen-qun-ju-lei" target="_self">
  239. <img src="https://api.limour.top/randomImg?d=2022-10-01 17:42:22" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】使用metacell进行分群聚类">
  240. </a>
  241. </div>
  242. <article class="col-12 col-md-8 mx-auto index-info">
  243. <h2 class="index-header">
  244. <a href="/shi-yong-metacell-jin-hang-fen-qun-ju-lei" target="_self">
  245. 【迁移】使用metacell进行分群聚类
  246. </a>
  247. </h2>
  248. <a class="index-excerpt " href="/shi-yong-metacell-jin-hang-fen-qun-ju-lei" target="_self">
  249. <div>
  250. 预处理 12345678910111213141516171819202122232425262728293031f_QC_plot &lt;- function(sce)&#123; options(repr.plot.width = 12, repr.plot.height = 6) print(Seurat::VlnPlot(sce, features = c(&quot;nFe
  251. </div>
  252. </a>
  253. <div class="index-btm post-metas">
  254. <div class="post-meta mr-3">
  255. <i class="iconfont icon-date"></i>
  256. <time datetime="2022-10-01 17:42" pubdate>
  257. 2022-10-01
  258. </time>
  259. </div>
  260. <div class="post-meta">
  261. <i class="iconfont icon-tags"></i>
  262. <a href="/tags/metacell/">#metacell</a>
  263. </div>
  264. </div>
  265. </article>
  266. </div>
  267. <div class="row mx-auto index-card">
  268. <div class="col-12 col-md-4 m-auto index-img">
  269. <a href="/shi-yong-FindTransferAnchors-dui-yang-ben-jin-hang-yu-zhu-shi" target="_self">
  270. <img src="https://api.limour.top/randomImg?d=2022-09-29 17:58:50" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】使用FindTransferAnchors对样本进行预注释">
  271. </a>
  272. </div>
  273. <article class="col-12 col-md-8 mx-auto index-info">
  274. <h2 class="index-header">
  275. <a href="/shi-yong-FindTransferAnchors-dui-yang-ben-jin-hang-yu-zhu-shi" target="_self">
  276. 【迁移】使用FindTransferAnchors对样本进行预注释
  277. </a>
  278. </h2>
  279. <a class="index-excerpt " href="/shi-yong-FindTransferAnchors-dui-yang-ben-jin-hang-yu-zhu-shi" target="_self">
  280. <div>
  281. 处理参考样本 12345678910111213ref_sce &lt;- readRDS(&#x27;~/upload/zl_liu/data/pca.rds&#x27;)ref_sce &lt;- subset(ref_sce, group == &#x27;CRPC&#x27;)table(ref_sce@meta.data$cell_type_fig3)g2m_genes &lt;- Se
  282. </div>
  283. </a>
  284. <div class="index-btm post-metas">
  285. <div class="post-meta mr-3">
  286. <i class="iconfont icon-date"></i>
  287. <time datetime="2022-09-29 17:58" pubdate>
  288. 2022-09-29
  289. </time>
  290. </div>
  291. <div class="post-meta">
  292. <i class="iconfont icon-tags"></i>
  293. <a href="/tags/findtransferanchors/">#FindTransferAnchors</a>
  294. </div>
  295. </div>
  296. </article>
  297. </div>
  298. <div class="row mx-auto index-card">
  299. <div class="col-12 col-md-4 m-auto index-img">
  300. <a href="/shi-yong-SCTransform-biao-zhun-hua" target="_self">
  301. <img src="https://api.limour.top/randomImg?d=2022-09-29 17:32:00" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】使用SCTransform标准化">
  302. </a>
  303. </div>
  304. <article class="col-12 col-md-8 mx-auto index-info">
  305. <h2 class="index-header">
  306. <a href="/shi-yong-SCTransform-biao-zhun-hua" target="_self">
  307. 【迁移】使用SCTransform标准化
  308. </a>
  309. </h2>
  310. <a class="index-excerpt " href="/shi-yong-SCTransform-biao-zhun-hua" target="_self">
  311. <div>
  312. 安装包 conda create -n seurat -c conda-forge r-seurat=4.1.1 -y conda activate seurat conda install -c conda-forge r-tidyverse -y conda install -c conda-forge r-irkernel -y Rscript -e “IRkernel::installs
  313. </div>
  314. </a>
  315. <div class="index-btm post-metas">
  316. <div class="post-meta mr-3">
  317. <i class="iconfont icon-date"></i>
  318. <time datetime="2022-09-29 17:32" pubdate>
  319. 2022-09-29
  320. </time>
  321. </div>
  322. <div class="post-meta">
  323. <i class="iconfont icon-tags"></i>
  324. <a href="/tags/sctransform/">#SCTransform</a>
  325. </div>
  326. </div>
  327. </article>
  328. </div>
  329. <div class="row mx-auto index-card">
  330. <div class="col-12 col-md-4 m-auto index-img">
  331. <a href="/shi-yong-Bootstrap-fa-ji-suan-zi-ju-zhi-xin-qu-jian" target="_self">
  332. <img src="https://api.limour.top/randomImg?d=2022-09-27 19:25:08" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】使用Bootstrap法计算自举置信区间">
  333. </a>
  334. </div>
  335. <article class="col-12 col-md-8 mx-auto index-info">
  336. <h2 class="index-header">
  337. <a href="/shi-yong-Bootstrap-fa-ji-suan-zi-ju-zhi-xin-qu-jian" target="_self">
  338. 【迁移】使用Bootstrap法计算自举置信区间
  339. </a>
  340. </h2>
  341. <a class="index-excerpt " href="/shi-yong-Bootstrap-fa-ji-suan-zi-ju-zhi-xin-qu-jian" target="_self">
  342. <div>
  343. 计算药物LD50用Bliss法最严谨,而改良寇氏法计算的结果误差也不大,因此做了一次改良寇氏法计算LD50的实验。最后需要计算一下结果的可信区间,于是来试试万能的Bootstrap法 安装包(这个例子用不上) conda activate MICE conda install -c conda-forge r-boot=1.3_28 -y 构造样本 组别 剂量 mg/kg 动物数 死亡数
  344. </div>
  345. </a>
  346. <div class="index-btm post-metas">
  347. <div class="post-meta mr-3">
  348. <i class="iconfont icon-date"></i>
  349. <time datetime="2022-09-27 19:25" pubdate>
  350. 2022-09-27
  351. </time>
  352. </div>
  353. <div class="post-meta">
  354. <i class="iconfont icon-tags"></i>
  355. <a href="/tags/bootstrap/">#Bootstrap</a>
  356. </div>
  357. </div>
  358. </article>
  359. </div>
  360. <div class="row mx-auto index-card">
  361. <div class="col-12 col-md-4 m-auto index-img">
  362. <a href="/cellranger-ding-liang--One-Library--Multiple-Flowcells" target="_self">
  363. <img src="https://api.limour.top/randomImg?d=2022-09-25 19:42:28" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】cellranger定量:One Library, Multiple Flowcells">
  364. </a>
  365. </div>
  366. <article class="col-12 col-md-8 mx-auto index-info">
  367. <h2 class="index-header">
  368. <a href="/cellranger-ding-liang--One-Library--Multiple-Flowcells" target="_self">
  369. 【迁移】cellranger定量:One Library, Multiple Flowcells
  370. </a>
  371. </h2>
  372. <a class="index-excerpt " href="/cellranger-ding-liang--One-Library--Multiple-Flowcells" target="_self">
  373. <div>
  374. 重命名R1、R2 原始数据质控 重命名前 ├── SRR12391722 │ ├── SRR12391722_1.fastq.gz │ └── SRR12391722_2.fastq.gz ├── SRR12391723 │ ├── SRR12391723_1.fastq.gz │ └── SRR12391723_2.fastq.gz ├── SRR12391724 │ ├── SRR1239
  375. </div>
  376. </a>
  377. <div class="index-btm post-metas">
  378. <div class="post-meta mr-3">
  379. <i class="iconfont icon-date"></i>
  380. <time datetime="2022-09-25 19:42" pubdate>
  381. 2022-09-25
  382. </time>
  383. </div>
  384. <div class="post-meta">
  385. <i class="iconfont icon-tags"></i>
  386. <a href="/tags/cellranger/">#cellranger</a>
  387. <a href="/tags/scvelo/">#scVelo</a>
  388. </div>
  389. </div>
  390. </article>
  391. </div>
  392. <div class="row mx-auto index-card">
  393. <div class="col-12 col-md-4 m-auto index-img">
  394. <a href="/cong-ENI-shu-ju-ku-xia-zai-fastq-wen-jian" target="_self">
  395. <img src="https://api.limour.top/randomImg?d=2022-09-25 19:32:17" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】从ENI数据库下载fastq文件">
  396. </a>
  397. </div>
  398. <article class="col-12 col-md-8 mx-auto index-info">
  399. <h2 class="index-header">
  400. <a href="/cong-ENI-shu-ju-ku-xia-zai-fastq-wen-jian" target="_self">
  401. 【迁移】从ENI数据库下载fastq文件
  402. </a>
  403. </h2>
  404. <a class="index-excerpt " href="/cong-ENI-shu-ju-ku-xia-zai-fastq-wen-jian" target="_self">
  405. <div>
  406. 从 ENI 数据库下载 进入ENA Browser,搜索对应的GSE号,进入study项目,选择TSV格式的Download report。 从TSV表格中提取下载链接,一行一个写入url.txt,前面加上ftp://,接着使用wget -c -i url.txt下载 批量重命名脚本: 1234ls *.fastq.gz | cut -d &#x27;_&#x27; -f 1 | while r
  407. </div>
  408. </a>
  409. <div class="index-btm post-metas">
  410. <div class="post-meta mr-3">
  411. <i class="iconfont icon-date"></i>
  412. <time datetime="2022-09-25 19:32" pubdate>
  413. 2022-09-25
  414. </time>
  415. </div>
  416. <div class="post-meta">
  417. <i class="iconfont icon-tags"></i>
  418. <a href="/tags/fastq/">#fastq</a>
  419. <a href="/tags/eni/">#ENI</a>
  420. <a href="/tags/ncbi-geo/">#NCBI-GEO</a>
  421. <a href="/tags/sra/">#SRA</a>
  422. </div>
  423. </div>
  424. </article>
  425. </div>
  426. <div class="row mx-auto index-card">
  427. <div class="col-12 col-md-4 m-auto index-img">
  428. <a href="/shi-yong--JTK-CYCLE--suan-fa-fen-xi-sheng-wu-jie-lv" target="_self">
  429. <img src="https://api.limour.top/randomImg?d=2022-09-19 20:17:29" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="【迁移】使用 JTK_CYCLE 算法分析生物节律">
  430. </a>
  431. </div>
  432. <article class="col-12 col-md-8 mx-auto index-info">
  433. <h2 class="index-header">
  434. <a href="/shi-yong--JTK-CYCLE--suan-fa-fen-xi-sheng-wu-jie-lv" target="_self">
  435. 【迁移】使用 JTK_CYCLE 算法分析生物节律
  436. </a>
  437. </h2>
  438. <a class="index-excerpt " href="/shi-yong--JTK-CYCLE--suan-fa-fen-xi-sheng-wu-jie-lv" target="_self">
  439. <div>
  440. JTK是一种非参数检测程序,能从芯片数据中检测循环转录本。除了计算每个转录本最佳的相位(LAG)、振幅(AMP)和周期(PER)外,JTK还计算了置换检验P值(ADJ.P)和Benjamini-Hochberg q值 (BH.Q)。与常规的周期检测算法相比,JTK具有更好的检验效能、更高的计算效率和更强的鲁棒性。R语言的metacycle包实现了ARSER、JTK_CYCLE、Lomb-Scarg
  441. </div>
  442. </a>
  443. <div class="index-btm post-metas">
  444. <div class="post-meta mr-3">
  445. <i class="iconfont icon-date"></i>
  446. <time datetime="2022-09-19 20:17" pubdate>
  447. 2022-09-19
  448. </time>
  449. </div>
  450. <div class="post-meta">
  451. <i class="iconfont icon-tags"></i>
  452. <a href="/tags/jtk-cycle/">#JTK_CYCLE</a>
  453. <a href="/tags/%E8%8A%82%E5%BE%8B/">#节律</a>
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