## ----include=TRUE, echo=FALSE, message=FALSE---------------------------------- knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, cache = FALSE) #str(knitr::opts_chunk$get()) ## ----fig.small = TRUE, echo = FALSE, fig.cap = 'gRNAs for Crispr/Cas9 (A) and Prime Editing'---- knitr::include_graphics("../inst/extdata/pe.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) ## ----fig.width=3.5, fig.height=1.5-------------------------------------------- # char_to_granges: Anzalone et al. (2019) prime editing targets require(multicrispr) bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 targets <- char_to_granges(c(PRNP = 'chr20:4699600:+'), bsgenome) plot_intervals(targets) ## ----fig.width=3.3, fig.height=1.7, message = FALSE, warning = FALSE---------- spacers <- find_primespacers(targets, bsgenome=bsgenome, edits = "T") ## ----------------------------------------------------------------------------- str(gr2dt(spacers), vec.len=2)