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CB2 is an R package which provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformati…

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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.

Update

Dec 4, 2020

If you are experiencing an issue during the installation, it would be possible due to multtest package hasn't been installed. If so, please use the following snippet to install the package.

install.package("BiocManager") # can be omitted if you have installed the package
install.packages("multtest")

May 26, 2020

  • Regarding #9, CB2 now provides logFC of gene-level analysis with two different modes. The default option is the same as the previous version, and setting logFC parameter value of measure_gene_stats to gene will provide the logFC calculate by gene-level CPMs.

April 14, 2020

  • Regarding #6, now users can use join_count_and_design function.

December 16, 2019

  • Regarding #4, CB2 now supports gzipped FASTQ file.
  • Regarding #5, calc_mappability() provide total_reads and mapped_reads columns.

July 2, 2019

There are several updates.

  • We have change the function name for the sgRNA-level test to measure_sgrna_stats. The original name run_estimation has been deprecated.
  • CB2 now supports a data.frame with character columns. In other words, you can use

How to install

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

install.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("LiuzLab/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)
      )
  }
}

MAP_FILE <- system.file("extdata", "toydata", "sg2gene.csv", package="CB2")
sgrna_count <- run_sgrna_quant(FASTA, df_design, MAP_FILE)
  
sgrna_stat <- measure_sgrna_stats(sgrna_count$count, df_design, 
                                  "Base", "Low", 
                                  ge_id = "gene",
                                  sg_id = "id")
gene_stat <- measure_gene_stats(sgrna_stat)

Or you could run the example with the following commented code.

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

More detailed tutorial is available here!

About

CB2 is an R package which provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformati…

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