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erccdashboard (version 1.6.0)

Assess Differential Gene Expression Experiments with ERCC Controls

Description

Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.

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Version

Version

1.6.0

License

GPL (>=2)

Issues

0

Pull Requests

0

Stars

7

Forks

6

Maintainer

Sarah Munro

Last Published

February 15th, 2017

Functions in erccdashboard (1.6.0)

ERCCMix1and2

ERCCMix1and2 dataframe
saveERCCPlots

Save erccdashboard plots to a pdf file
ERCCDef

ERCCDef dataframe
est_r_m

Estimate the mRNA fraction differences for the pair of samples using replicate data
UHRR.HBRR.countDat

UHRR and HBRR RNA-Seq Illumina count data
UHRR.HBRR.totalReads

UHRR and HBRR sample total read data
maSignal

Generate MA plots with or without annotation using LODR estimates
MET.CTL.totalReads

Rat toxicogenomics total read data
geneExprTest

Prepare differential expression testing results for spike-in analysis
dynRangePlot

Produce signal-abundance plot to evaluate dynamic range
SEQC.Example

Example data from SEQC project for erccdashboard analysis
erccROC

Produce Receiver Operator Characteristic (ROC) Curves and AUC statistics
annotLODR

Annotate signal-abundance and ratio-abundance plots with LODR
ERCC

ERCC data
MET.CTL.countDat

Rat toxicogenomics count data
runDashboard

Run default erccdashboard analysis of ERCC control ratio mixtures
UHRR.HBRR.arrayDat

UHRR and HBRR Illumina BeadArray data
estLODR

Estimate Limit of Detection of Ratios (LODR)
initDat

Initialize the exDat list