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# General
#========
# Install azimuth for scoring
#----------------------------
# require(reticulate)
# conda_create('azienv', c('python=2.7'))
# use_condaenv('azienv')
# py_install(c('azimuth', 'scikit-learn==0.17.1'), 'azienv', pip = TRUE)
# reticulate::use_condaenv('azienv')
# Index genome
#-------------
require(multicrispr)
index_genome(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
index_genome(BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38)
# Load packages
require(magrittr)
require(multicrispr)
reticulate::use_condaenv('azienv')
# Parallel Targeting
#===================
# Define targets to block TFBS
bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr')
targets <- bed_to_granges(bedfile, 'mm10') %>%
extend(-22, +22)
# Find specific, efficient spacers
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
spacers <- find_spacers(targets, bsgenome)
spacers %<>% filter_target_specific(targets, bsgenome)
spacers %<>% add_efficiency(bsgenome, method = 'Doench2016')
spacers
# Prime Editing
#==============
# Define target for editing
bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
targets <- char_to_granges(c( PRNP = 'chr20:4699600:+', # snp
HBB = 'chr11:5227002:-', # snp
HEXA = 'chr15:72346580-72346583:-', # del
CFTR = 'chr7:117559593-117559595:+'), # ins
bsgenome)
# Find specific, efficient spacers
spacers <- find_primespacers(targets, bsgenome)
spacers %<>% filter_prime_specific(bsgenome)
spacers %<>% add_efficiency(bsgenome, method = 'Doench2016')
spacers
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