# CRISPR Screen and Gene Expression Differential Analysis

## Documentation for package ‘CEDA’ version 1.1.1

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

## Help Pages

alphaBeta | Calculating a significance score of a gene based on the corresponding sgRNAs' p-values of the gene.
calculateGeneLFC | Calculating gene-level log fold ratios
calculateGenePval | Calculating gene level p-values using modified robust rank aggregation (alpha-RRA method) on sgRNAs' p-values
densityPlot | 2D density contour plot of gene log2 fold ratios against gene expression levels
EMFit | Fitting multi-component normal mixture models by R package mixtools
makeRhoNull | Generating the null distribution of the significance score of a gene.
mda231 | CRISPR screen data of cell line MDA-MB-231.
medianNormalization | Median normalization of sgRNA counts
normalMM | Performing empirical Bayes modeling on limma results
permuteLimma | Modeling CRISPR data with a permutation test between conditions by R package limma
preparePlotData | Prepare data for density plot and ridge plot
ridgePlot | Density ridgeline plot of gene expression levels for different FDR groups.
runLimma | Modeling CRISPR screen data by R package limma
scatterPlot | Scatter plot of log2 fold ratios against gene expression levels