NOTE: this repo is now part of breakinspectoR. The code here has been frozen as of November 2024, and additional features are available only in breakinspectoR.
Prediction of blunt rates of Streptococcus pyogenes Cas9 (SpCas9) using the XGBoost model trained with HiPlex1 data.
The main dependency is H2O.
Remove any previously installed H2O packages for R.
if ("package:h2o" %in% search()) { detach("package:h2o", unload=TRUE) }
if ("h2o" %in% rownames(installed.packages())) { remove.packages("h2o") }Download packages that H2O depends on.
install.packages(c("RCurl","jsonlite"))Download and install the H2O package for R. The models were trained on H2O version 3.36.1.2, therefore specifically install this version.
install.packages("h2o", type="source", repos="http://h2o-release.s3.amazonaws.com/h2o/rel-zumbo/2/R")Test the H2O installation with:
library(h2o)
localH2O = h2o.init()
demo(h2o.kmeans)Now, it's all set to install the package.
The package resides in GitHub only. You will probably need devtools for that (install.packages("devtools")).
devtools::install_github("roukoslab/bluntPred")Open the web app in your R console:
bluntPred::shiny_bluntPred()Paste a list of gRNAs targets and click on Predict.
The list can actually be a table with <tab> or <comma> separated fields.
The gRNA sequence is expected to be in the first column.
NOTE: Only the seed portion of the protospacer (this is, the last 10 nucloetides of the target sequence) are used for the prediction in this model.
If you find this tool useful and use it in your research, please cite our publication:
Longo, Sayols et al., Linking CRISPR–Cas9 double-strand break profiles to gene editing precision with BreakTag. Nat. Biotechnol. 2024. DOI: https://doi.org/10.1038/s41587-024-02238-8