What is CB2

CB2(CRISPRBetaBinomial) is a new algorithm for analyzing CRISPR data based on beta-binomial distribution. We provide CB2 as a R package, and the interal algorithms of CB2 are also implemented in CRISPRCloud.

How to install

Currently CB2 is now on CRAN, and you can install it using install.package function.

instll.package("CB2")

Installation Github version of CB2 can be done using the following lines of code in your R terminal.

install.packages("devtools")
devtools::install_github("hyunhwaj/CB2")

Alternatively, here is a one-liner command line for the installation.

Rscript -e "install.packages('devtools'); devtools::install_github('LiuzLab/CB2')"

A simple example how to use CB2 in R

FASTA <- system.file("extdata", "toydata",
                     "small_sample.fasta",
                     package = "CB2")
df_design <- data.frame()
for(g in c("Low", "High", "Base")) {
  for(i in 1:2) {
    FASTQ <- system.file("extdata", "toydata",
                         sprintf("%s%d.fastq", g, i), 
                         package = "CB2")
    df_design <- rbind(df_design, 
      data.frame(
        group = g, 
        sample_name = sprintf("%s%d", g, i),
        fastq_path = FASTQ, 
        stringsAsFactors = F)
      )
  }
}

sgrna_count <- run_sgrna_quant(FASTA, df_design)
sgrna_stat <- run_estimation(sgrna_count$count, df_design, "Base", "Low")
gene_stat <- measure_gene_stats(sgrna_stat)