CRISPR Screen and Gene Expression Differential Analysis

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Documentation for package ‘CEDA’ version 1.0.2

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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
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 MD231.
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
runLimma Modeling CRISPR screen data by R package limma
scatterPlot Scatter plot of log2 fold ratios against gene expression levels