{"id":25121,"date":"2024-01-18T16:46:49","date_gmt":"2024-01-18T08:46:49","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25121"},"modified":"2024-01-18T16:46:52","modified_gmt":"2024-01-18T08:46:52","slug":"%e6%83%b3%e7%9f%a5%e9%81%93%e7%bb%86%e8%83%9e%e5%88%86%e5%8c%96%e8%bd%a8%e8%bf%b9%ef%bc%9fvelocyto%e6%9d%a5%e5%b8%ae%e4%bd%a0%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25121","title":{"rendered":"\u60f3\u77e5\u9053\u7ec6\u80de\u5206\u5316\u8f68\u8ff9\uff1fvelocyto\u6765\u5e2e\u4f60\uff01"},"content":{"rendered":"

\u5728\u751f\u547d\u7684\u751f\u957f\u53d1\u80b2\u8fc7\u7a0b\u4e2d\uff0c\u7ec6\u80de\u90fd\u5728\u4e0d\u65ad\u4ece\u4e00\u79cd\u72b6\u6001\u8fc7\u6e21\u5230\u53e6\u4e00\u79cd\u72b6\u6001\uff0c\u8868\u8fbe\u4e0d\u540c\u7684\u57fa\u56e0\uff0c\u4ea7\u751f\u86cb\u767d\u7ec4\u548c\u4ee3\u8c22\u7269\u7684\u52a8\u6001\u91cd\u590d\u3002\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u8f68\u8ff9\u63a8\u65ad\u7684\u65b9\u6cd5\uff0c\u6839\u636e\u6d4b\u5e8f\u7ec6\u80de\u77ac\u65f6\u72b6\u6001\u4e4b\u95f4\u8868\u8fbe\u6a21\u5f0f\u7684\u76f8\u4f3c\u6027\u5bf9\u5355\u7ec6\u80de\u6cbf\u7740\u8f68\u8ff9\u8fdb\u884c\u6392\u5e8f\uff0c\u4ee5\u6a21\u62df\u7ec6\u80de\u52a8\u6001\u53d8\u5316\u7684\u8fc7\u7a0b\u3002<\/p>\n

\u4eca\u5929\u8981\u4ecb\u7ecd\u7684RNA \u901f\u7387\u5206\u6790\uff08RNA velocity\uff09\u57fa\u4e8e\u771f\u5b9e\u7684\u8f6c\u5f55\u52a8\u529b\u5b66\uff0c\u53ef\u7528\u4e8e\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u7684\u52a8\u6001\u5206\u5316\u7684\u7814\u7a76\u3002\u901a\u8fc7\u62df\u5408\u524d\u4f53\uff08\u672a\u526a\u63a5\u7684\uff09\u548c\u6210\u719f\uff08\u526a\u63a5\u7684\uff09mRNA \u4e30\u5ea6\u4e4b\u95f4\u7684\u6bd4\u503c\u6765\u83b7\u5f97\u57fa\u56e0\u7279\u5f02\u6027\u901f\u5ea6\uff0c\u5f97\u51fa\u53ef\u80fd\u7684\u7ec6\u80de\u72b6\u6001\u53d8\u5316\uff0c\u4ece\u800c\u8ffd\u6eaf\u7ec6\u80de\u7684\u8d77\u6e90\u548c\u6f5c\u5728\u7684\u547d\u8fd0\uff0c\u4f18\u70b9\u5728\u4e8e\u8fd9\u4e2a\u65b9\u6cd5\u4e0d\u9700\u8981\u6307\u5b9a\u8d77\u70b9\u548c\u7ec8\u70b9\uff0c\u53ef\u4ee5\u5bf9\u672a\u77e5\u5206\u5316\u5173\u7cfb\u7684\u7ec6\u80de\u8fdb\u884c\u5206\u6790\u3002<\/p>\n

\u63a5\u4e0b\u6765\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6df1\u5165\u4e86\u89e3\u4e00\u4e0b\u8fd9\u4e2a\u65b9\u6cd5\u5427\uff01<\/p>\n

RNA velocity\u6240\u9700\u8981\u7684\u5305\u548c\u4e4b\u524d\u4ecb\u7ecd\u7684SCENIC\u4e00\u6837\uff0c\u4e5f\u6709python\u548cR\u7684\u7248\u672c\uff0c\u6211\u4eec\u8fd9\u91cc\u4ecb\u7ecdR\u5305velocyto.R\u7684\u5b89\u88c5\u3002<\/p>\n

\u5b98\u65b9\u6307\u8defhttps:\/\/github.com\/velocyto-team\/velocyto.R<\/p>\n

library(devtools)<\/p>\n

install_github(“velocyto-team\/velocyto.R”)<\/p>\n

#\u6ce8\u610f\uff0c\u5982\u679c\u7cfb\u7edf\u6ca1\u6709\u5b89\u88c5boost\u5e93\uff0c\u9700\u8981\u63d0\u524d\u5b89\u88c5\u4e00\u4e0b\uff0c\u4f8b\u5982\uff1a<\/p>\n

sudo apt-get install libboost-dev<\/p>\n

\u5bf9\u4e8e\u8f93\u5165\u6587\u4ef6\uff0c\u6709\u4ee5\u4e0b\u4e09\u79cd\u683c\u5f0f\u53ef\u9009\uff1a<\/p>\n

    \n
  1. \u6765\u81eaSMART-seq2\u7684bam\u6587\u4ef6<\/li>\n
  2. loom\u6587\u4ef6\uff0c\u53ef\u7531cellranger\u8dd1\u51fa\uff0c\u6216scanpy\u4fdd\u5b58<\/li>\n
  3. dropEst\u7684matrices\uff0c\u8fd9\u4e2a\u65b9\u6cd5\u7528\u5f97\u6bd4\u8f83\u5c11\uff0c\u8fd9\u91cc\u5c31\u4e0d\u7ec6\u8bf4\u5566\u3002<\/li>\n<\/ol>\n

    \u6211\u4eec\u8fd9\u91cc\u9009\u62e92\u7684\u65b9\u6cd5\uff0c\u8bfb\u53d6loom\u6587\u4ef6\u7684\u683c\u5f0f~<\/p>\n

    ldat <-read.loom.matrices(“sample.loom”)<\/p>\n

    <\/p>\n

    \u8be5\u6587\u4ef6\u5305\u542bspliced\uff08\u4e0d\u5305\u542b\u5185\u542b\u5b50\uff09\uff0cunspliced\uff08\u5305\u542b\u5185\u542b\u5b50\uff09\u548cambiguous\uff08\u5728\u5206\u6790\u4e2d\u4e0d\u4f1a\u88ab\u4f7f\u7528\uff09\u4e09\u4e2aelements\u7684list<\/p>\n

    #\u63d0\u53d6spliced\u4e0eunspliced\u6587\u4ef6<\/p>\n

    emat <- ldat$spliced #\u5916\u663e\u5b50(spliced)\u8868\u8fbe\u77e9\u9635<\/p>\n

    nmat <- ldat$unspliced #\u5185\u542b\u5b50(unspliced)\u8868\u8fbe\u77e9\u9635<\/p>\n

    #\u63d0\u53d6Seurat\u5bf9\u8c61\u7684UMAP\u4fe1\u606f<\/p>\n

    load(\u201csce.RData\u201d) #sce\u4e3a\u5f85\u5206\u6790\u7684Seurat\u5bf9\u8c61<\/p>\n

    umap <- sce@reductions$umap@cell.embeddings<\/p>\n

    #\u4f30\u8ba1\u7ec6\u80de\u95f4\u8ddd\u79bb<\/p>\n

    cell.dist <- as.dist(1-armaCor(t(sce@reductions$umap@cell.embeddings)))<\/p>\n

    fit.quantile <- 0.02<\/p>\n

    rvel.cd <- gene.relative.velocity.estimates(emat, nmat, deltaT=2, kCells=10,<\/p>\n

    cell.dist=cell.dist,fit.quantile=fit.quantile,n.cores=24)<\/p>\n

    #\u5728UMAP\u56fe\u4e0a\u7ed8\u5236RNA velocity<\/p>\n

    pdf(“velocity.pdf”,height=6,width=8)<\/p>\n

    pic <- UMAPPlot(sce)<\/p>\n

    ggplot_build(pic)$data<\/p>\n

    colors <- as.list(ggplot_build(pic)$data[[1]]$colour)<\/p>\n

    names(colors) <- rownames(umap)<\/p>\n

    p<- show.velocity.on.embedding.cor(umap, rvel.cd, n=30, scale=’sqrt’,<\/p>\n

    cell.colors=ac(colors,alpha=0.5),cex=0.8,arrow.scale=2,<\/p>\n

    show.grid.flow=T,min.grid.cell.mass=1.0,grid.n=50,<\/p>\n

    arrow.lwd=1,do.par=F,<\/p>\n

    cell.border.alpha =0.1,USE_OPENMP=1,<\/p>\n

    n.cores=24,main=”Cell Velocity”)<\/p>\n

    dev.off()<\/p>\n

    \u501f\u7528\u5b98\u65b9\u6559\u7a0b\u4e2d\u7684\u56fe\u7247\uff0c\u6211\u4eec\u53ef\u4ee5\u5f97\u5230\u7c7b\u4f3c\u8fd9\u6837\u7684\u7ed3\u679c<\/p>\n

    <\/p>\n

    \u6b64\u5916\uff0c\u5982\u679c\u4f7f\u7528\u5df2\u6ce8\u91ca\u7684\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\uff0c\u6211\u4eec\u53ef\u4ee5\u77e5\u9053\u5404\u79cd\u7c7b\u578b\u7684\u7ec6\u80de\u5206\u5316\u662f\u5982\u4f55\u968f\u65f6\u95f4\u8fdb\u884c\u7684\u3002\u5982\u4e0b\u56fe\u6765\u6e90\u4e8eNature\u6587\u7ae0\u300aRNA velocity of single cells\u300b\uff0c\u53ef\u4ee5\u5f97\u77e5\u9897\u7c92\u7ec6\u80de\u662f\u7531\u6210\u795e\u7ecf\u7ec6\u80de\u5206\u5316\u800c\u6765\u3002<\/p>\n

    <\/p>\n

    \u600e\u4e48\u6837\uff0c\u662f\u4e0d\u662f\u5f88\u795e\u5947\u5462\uff1f\u5feb\u5feb\u7528\u8d77\u6765\u5427\uff01\u90a3\u4e48\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u4e86~<\/p>\n

    \u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1-\u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/p>\n

    \u670d\u52a1\u5668\u4f7f\u7528\u53ef\u4ee5\u8054\u7cfb\u5fae\u4fe1\uff1a18502195490<\/p>\n","protected":false},"excerpt":{"rendered":"

    \u5728\u751f\u547d\u7684\u751f\u957f\u53d1\u80b2\u8fc7\u7a0b\u4e2d\uff0c\u7ec6\u80de\u90fd\u5728\u4e0d\u65ad\u4ece\u4e00\u79cd\u72b6\u6001\u8fc7\u6e21\u5230\u53e6\u4e00\u79cd\u72b6\u6001\uff0c\u8868\u8fbe\u4e0d\u540c\u7684\u57fa\u56e0\uff0c\u4ea7\u751f\u86cb\u767d\u7ec4\u548c\u4ee3\u8c22\u7269\u7684\u52a8\u6001\u91cd\u590d\u3002 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25121"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=25121"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25121\/revisions"}],"predecessor-version":[{"id":25125,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25121\/revisions\/25125"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25121"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25121"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25121"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}