# Assess Differential Gene Expression Experiments with ERCC Controls

## Documentation for package ‘erccdashboard’ version 1.12.1

- 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