Commit 24a4011e authored by aditya.bhagwat's avatar aditya.bhagwat
Browse files

Updated README

parent 633c8f0a
<center> <h1> multicrispr </h1> </center>
![](https://gitlab.gwdg.de/loosolab/software/multicrispr/wikis/uploads/43b432cd32eb156af2ac217efd98aceb/workflow.png)
1. Read a set of genomics ranges
2. Find cas9 sequences which
- target
+ **thousands** of such **ranges**, their **flanks**, or **slopped extensions**
+ **efficiently** with **data.table** and **Biostrings** based **c-level** looping and matching
+ enabling **crispr<sub>ko</sub>**, **crispr<sub>i</sub>**, and **crispr<sub>a</sub>** design.
- are free of offtarget (mis)matches
- bind well
+ as determined by Doench 2016 ontargetscore (interfacing to original python module **azimuth** when available)
+ or Doench 2014 ontargetscore otherwise
remotes::install_git('https://gitlab.gwdg.de/loosolab/software/multicrispr.git',
repos = BiocManager::repositories())
### Overview
![](https://gitlab.gwdg.de/loosolab/software/multicrispr/wikis/uploads/ff69d25a1cad1f4c93fdf79e0c549ecf/readme.png)
### Installation
# Install multicrispr
remotes::install_git('https://gitlab.gwdg.de/loosolab/software/multicrispr.git',
repos = BiocManager::repositories())
# Install azimuth
install.packages('reticulate')
reticulate::conda_create('azienv', c('python=2.7'))
reticulate::use_condaenv('azienv')
reticulate::py_install(c('azimuth', 'scikit-learn==0.17.1'), 'azienv', pip = TRUE)
# Index mm10 and hg38
BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg38')
index_genome(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
index_genome(BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38)
### Use
# Parallel Targeting
reticulate::use_condaenv('azienv')
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
bedfile <- system.file('extdata/SRF.bed', package='multicrispr')
targets <- multicrispr::bed_to_granges(bedfile, genome='mm10')
extended <- extend(targets, -22, +22)
spacers <- extended %>% find_spacers(bsgenome)
spacers %<>% add_specificity(extended, bsgenome)
spacers %<>% add_efficiency(bsgenome, method = 'Doench2016')
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment