CRISPR Pooled Screen Analysis using Beta-Binomial Test
A function to calculate the mappabilities of each NGS sample.
A C++ function to perform a parameter estimation for the sgRNA-level t...
A function to normalize sgRNA read counts.
A function to join a count table and a design table.
A function to perform gene-level test using a sgRNA-level statistics.
A function to perform a statistical test at a sgRNA-level
A function to show a heatmap sgRNA-level corrleations of the NGS sampl...
A function to plot read count distribution.
A function to visualize dot plots for a gene.
A function to plot the first two principal components of samples.
A C++ function to quantify sgRNA abundance from NGS samples.
A function to perform a statistical test at a sgRNA-level, deprecated.
A function to run a sgRNA quantification algorithm from NGS sample
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/bioinformatics/btg173>.