erccdashboard: Assess Differential Gene Expression Experiments with ERCC Controls

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

Author
Sarah Munro, Steve Lund
Date of publication
None
Maintainer
Sarah Munro <sarah.munro@nist.gov>
License
GPL (>=2)
Version
1.8.0
URLs

View on Bioconductor

Man 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...
estLODR
Estimate Limit of Detection of Ratios (LODR)
est_r_m
Estimate the mRNA fraction differences for the pair of...
geneExprTest
Prepare differential expression testing results for spike-in...
initDat
Initialize the exDat list
maSignal
Generate MA plots with or without annotation using LODR...
MET.CTL.countDat
Rat toxicogenomics count data
MET.CTL.totalReads
Rat toxicogenomics total read data
runDashboard
Run default erccdashboard analysis of ERCC control ratio...
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

Files in this package

erccdashboard/DESCRIPTION
erccdashboard/NAMESPACE
erccdashboard/NEWS
erccdashboard/R
erccdashboard/R/annotLODR.R
erccdashboard/R/dashboardFile.R
erccdashboard/R/dynRangePlot.R
erccdashboard/R/erccROC.R
erccdashboard/R/estLODR.R
erccdashboard/R/est_r_m.R
erccdashboard/R/geneExprTest.R
erccdashboard/R/getDesignMat.R
erccdashboard/R/initDat.R
erccdashboard/R/loadERCCInfo.R
erccdashboard/R/loadExpMeas.R
erccdashboard/R/maSignal.R
erccdashboard/R/normalizeDat.R
erccdashboard/R/plotAdjust.R
erccdashboard/R/prepERCCDat.R
erccdashboard/R/printLODRres.R
erccdashboard/R/runDashboard.R
erccdashboard/R/saveERCCPlots.R
erccdashboard/R/testDEArray.R
erccdashboard/R/testDECount.R
erccdashboard/build
erccdashboard/build/vignette.rds
erccdashboard/data
erccdashboard/data/ERCC.RData
erccdashboard/data/SEQC.Example.RData
erccdashboard/data/datalist
erccdashboard/inst
erccdashboard/inst/CITATION
erccdashboard/inst/doc
erccdashboard/inst/doc/erccdashboard.R
erccdashboard/inst/doc/erccdashboard.Rnw
erccdashboard/inst/doc/erccdashboard.pdf
erccdashboard/man
erccdashboard/man/ERCC.Rd
erccdashboard/man/ERCCDef.Rd
erccdashboard/man/ERCCMix1and2.Rd
erccdashboard/man/MET.CTL.countDat.Rd
erccdashboard/man/MET.CTL.totalReads.Rd
erccdashboard/man/SEQC.Example.Rd
erccdashboard/man/UHRR.HBRR.arrayDat.Rd
erccdashboard/man/UHRR.HBRR.countDat.Rd
erccdashboard/man/UHRR.HBRR.totalReads.Rd
erccdashboard/man/annotLODR.Rd
erccdashboard/man/dynRangePlot.Rd
erccdashboard/man/erccROC.Rd
erccdashboard/man/estLODR.Rd
erccdashboard/man/est_r_m.Rd
erccdashboard/man/geneExprTest.Rd
erccdashboard/man/initDat.Rd
erccdashboard/man/maSignal.Rd
erccdashboard/man/runDashboard.Rd
erccdashboard/man/saveERCCPlots.Rd
erccdashboard/vignettes
erccdashboard/vignettes/erccdashboard.Rnw