Assess Differential Gene Expression Experiments with ERCC Controls


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Documentation for package ‘erccdashboard’ version 1.16.1

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