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 |