# #——包括= TRUE,呼应= FALSE,消息= FALSE --------------------------------- knitr: opts_chunk美元集(呼应= TRUE,崩溃= TRUE,缓存= FALSE) # str (knitr: opts_chunk获得美元 ()) ## ---- fig.normal = TRUE,回声= FALSE ----------------------------------------- knitr: include_graphics(“. . /本月/ extdata / crispr.png ") ## ---- 概述、fig.wide = TRUE。宽度=“100%”,回声= FALSE -------------- knitr: include_graphics(“. . /本月/ extdata / overview.png ") ## ---- eval = FALSE ------------------------------------------------------------ # # 从BioC # install.packages (BiocManager) # BiocManager::安装(version =“重击”)# BiocManager::安装(“multicrispr”)从gitlab # # #:# # < url -“https://gitlab.gwdg.de/loosolab/software/multicrispr.git”# #遥控器::install_git (url,回购= BiocManager::存储库 ()) ## ---- eval = FALSE ------------------------------------------------------------ # # 安装一次# #网状::conda_create (azienv, python = 2.7) # #网状::conda_install(“azienv”、“方位”,pip = TRUE) # #网状::conda_install(‘azienv’,‘scikit-learn = = 0.17.1’,皮普= TRUE) # # #网状激活::use_condaenv(“azienv ') ## ---- eval = FALSE ------------------------------------------------------------ # index_genome (BSgenome.Mmusculus.UCSC.mm10:: BSgenome.Mmusculus.UCSC.mm10) # index_genome (BSgenome.Hsapiens.UCSC.hg38:: BSgenome.Hsapiens.UCSC。hg38) ## ---- echo =FALSE, results =FALSE, message=FALSE---------------------------- #不需要# Done to load dependencies silent - keeping focus #require(GenomicRanges) #require(Biostrings) #require(dplyr) #require(dbplyr) #require(htmltools) #require(htmlwidgets) ## ---- message=FALSE, out。宽度= " 60 %"------------------------------------------ 需要(magrittr)要求(multicrispr) bedfile < -执行(“extdata / SRF。bed'， package = 'multicrispr') targets0 <- bed_to_granges(bedfile, genome = 'mm10') ## ---- message=FALSE, out。宽度= " 60 %"------------------------------------------ entrezfile < -执行(“extdata / SRF。entrez'， package = 'multicrispr') txdb <- txdb . mmusculus . ucsc .mm10. knowngene:: txdb . mmusculus . ucsc .mm10。knownGene invisible(genefile_to_granges(entrezfile, txdb, complement = TRUE)) ## ---- fig.width=3.5, fig.height=1.5, out。宽度= " 50 %"-------------------------- bsgenome < - BSgenome.Mmusculus.UCSC.mm10:: BSgenome.Mmusculus.UCSC。mm10 plot_interval (char_to_granges(c(srf1 = 'chr13:119991554-119991569:+')， bsgenome)) ## ---- fig.wide = TRUE, fig.show = 'hold'， message = FALSE, out。宽度=“60%”,fig.width = 7, fig.height = 3——#旁边看不见(up_flank (targets0, -200,(1) #下侧面看不见(down_flank (targets0, 200)) #双侧面看不见(double_flank (targets0 -200, 1 + 1, + 200)) #扩展目标< -扩展(targets0, -22, 22日= TRUE ) ## ---- 消息= FALSE ----------------------------------------------------------- 逆电流器< - find_spacers(目标,bsgenome补充= FALSE,不匹配= 0,subtract_targets = TRUE ) ## ----------------------------------------------------------------------------- str (gr2dt(衬垫),vec.len = 2)