Assess Differential Gene Expression Experiments with ERCC Controls

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Documentation for package ‘erccdashboard’ version 1.40.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotLODR	Annotate signal-abundance and ratio-abundance plots with LODR
dynRangePlot	Produce signal-abundance plot to evaluate dynamic range
ERCC	ERCC data
ERCCDef	ERCCDef dataframe
ERCCMix1and2	ERCCMix1and2 dataframe
erccROC	Produce Receiver Operator Characteristic (ROC) Curves and AUC statistics
estLODR	Estimate Limit of Detection of Ratios (LODR)
est_r_m	Estimate the mRNA fraction differences for the pair of samples using replicate data
geneExprTest	Prepare differential expression testing results for spike-in analysis
initDat	Initialize the exDat list
maSignal	Generate MA plots with or without annotation using LODR estimates
MET.CTL.countDat	Rat toxicogenomics count data
MET.CTL.totalReads	Rat toxicogenomics total read data
runDashboard	Run default erccdashboard analysis of ERCC control ratio mixtures
saveERCCPlots	Save erccdashboard plots to a pdf file
SEQC.Example	Example data from SEQC project for erccdashboard analysis
UHRR.HBRR.arrayDat	UHRR and HBRR Illumina BeadArray data
UHRR.HBRR.countDat	UHRR and HBRR RNA-Seq Illumina count data
UHRR.HBRR.totalReads	UHRR and HBRR sample total read data