# CRISPR Pooled Screen Analysis using Beta-Binomial Test

## Documentation for package ‘CB2’ version 1.3.8

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

calc_mappability | A function to calculate the mappabilities of each NGS sample.
Evers_CRISPRn_RT112 | A benchmark CRISPRn pooled screen data from Evers et al.
fit_ab | A C++ function to perform a parameter estimation for the sgRNA-level test. It will estimate two different parameters 'phat' and 'vhat,' and we assume input count data follows the beta-binomial distribution. Dr. Keith Baggerly initially implemented this code in Matlab, and it has been rewritten it in C++ for the speed-up.
get_CPM | A function to normalize sgRNA read counts.
join_count_and_design | A function to join a count table and a design table.
measure_gene_stats | A function to perform gene-level test using a sgRNA-level statistics.
measure_sgrna_stats | A function to perform a statistical test at a sgRNA-level
plot_corr_heatmap | A function to show a heatmap sgRNA-level corrleations of the NGS samples.
plot_count_distribution | A function to plot read count distribution.
plot_dotplot | A function to visualize dot plots for a gene.
plot_PCA | A function to plot the first two principal components of samples.
quant | A C++ function to quantify sgRNA abundance from NGS samples.
rep_row | Repeat a row
run_estimation | A function to perform a statistical test at a sgRNA-level, deprecated.
run_sgrna_quant | A function to run a sgRNA quantification algorithm from NGS sample
Sanson_CRISPRn_A375 | A benchmark CRISPRn pooled screen data from Sanson et al.