Nothing
## ---- 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)
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