Learn R Programming

CEDA

Copy Link

Version

Install

install.packages('CEDA')

Monthly Downloads

221

Version

1.1.1

License

Apache License (== 2.0)

Maintainer

Lianbo Yu

Last Published

February 27th, 2024

Functions in CEDA (1.1.1)

densityPlot

2D density contour plot of gene log2 fold ratios against gene expression levels
calculateGeneLFC

Calculating gene-level log fold ratios
makeRhoNull

Generating the null distribution of the significance score of a gene.
medianNormalization

Median normalization of sgRNA counts
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
permuteLimma

Modeling CRISPR data with a permutation test between conditions by R package limma
alphaBeta

Calculating a significance score of a gene based on the corresponding sgRNAs' p-values of the gene.
normalMM

Performing empirical Bayes modeling on limma results
mda231

CRISPR screen data of cell line MDA-MB-231.
runLimma

Modeling CRISPR screen data by R package limma
scatterPlot

Scatter plot of log2 fold ratios against gene expression levels
preparePlotData

Prepare data for density plot and ridge plot
ridgePlot

Density ridgeline plot of gene expression levels for different FDR groups.