## ---- include=TRUE, echo=FALSE, message=FALSE--------------------------------- knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, cache = TRUE) #str(knitr::opts_chunk$get()) ## ---- fig.normal = TRUE, echo = FALSE----------------------------------------- knitr::include_graphics("../inst/extdata/crispr.png") ## ----overview, fig.wide = TRUE, out.width = "100%", echo = FALSE-------------- knitr::include_graphics("../inst/extdata/overview.png") ## ---- eval = FALSE------------------------------------------------------------ # # From BioC # install.packages("BiocManager") # BiocManager::install(version='devel') # BiocManager::install("multicrispr") # # # From gitlab: # #url <- 'https://gitlab.gwdg.de/loosolab/software/multicrispr.git' # #remotes::install_git(url, repos = BiocManager::repositories()) ## ---- eval = FALSE------------------------------------------------------------ # # Install once # # reticulate::conda_create('azienv', 'python=2.7') # # reticulate::conda_install('azienv', 'azimuth', pip = TRUE) # # reticulate::conda_install('azienv', 'scikit-learn==0.17.1', pip = TRUE) # # Then activate # reticulate::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---------------------------- # Not required # Done to load dependencies silently - keeping focus #require(GenomicRanges) #require(Biostrings) #require(dplyr) #require(dbplyr) #require(htmltools) #require(htmlwidgets) ## ---- message=FALSE, out.width="60%"------------------------------------------ require(magrittr) require(multicrispr) bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr') targets0 <- bed_to_granges(bedfile, genome = 'mm10') ## ---- message=FALSE, out.width="60%"------------------------------------------ entrezfile <- system.file('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.width="50%"-------------------------- bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 plot_intervals(char_to_granges(c(srf1 = 'chr13:119991554-119991569:+'), bsgenome)) ## ---- fig.wide = TRUE, fig.show = 'hold', message = FALSE, out.width="60%", fig.width=7, fig.height=3---- # Up flank invisible(up_flank( targets0, -200, -1)) # Down flank invisible(down_flank( targets0, 1, 200)) # Double flank invisible(double_flank(targets0, -200, -1, +1, +200)) # Extend targets <- extend(targets0, -22, 22, plot = TRUE) ## ---- message=FALSE----------------------------------------------------------- spacers <- find_spacers( targets, bsgenome, complement=FALSE, mismatches=0, subtract_targets = TRUE) ## ----------------------------------------------------------------------------- str(gr2dt(spacers), vec.len=2)