erccdashboard: Assess Differential Gene Expression Experiments with ERCC Controls
Version 1.10.0

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

Browse man pages Browse package API and functions Browse package files

AuthorSarah Munro, Steve Lund
Bioconductor views AlternativeSplicing BatchEffect DifferentialExpression DifferentialSplicing GeneExpression Genetics Microarray MultipleComparison QualityControl RNASeq Transcription mRNAMicroarray
Date of publicationNone
MaintainerSarah Munro <sarah.munro@nist.gov>
LicenseGPL (>=2)
Version1.10.0
URL http://www.nist.gov/mml/bbd/erccdashboard.cfm https://github.com/usnistgov/erccdashboard http://tinyurl.com/erccsrm
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("erccdashboard")

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

Functions

ERCC Man page
ERCCDef Man page
ERCCMix1and2 Man page
MET.CTL.countDat Man page
MET.CTL.totalReads Man page
SEQC.Example Man page
UHRR.HBRR.arrayDat Man page
UHRR.HBRR.countDat Man page
UHRR.HBRR.totalReads Man page
annotLODR Man page Source code
dashboardFile Source code
dynRangePlot Man page Source code
erccROC Man page Source code
estLODR Man page Source code
est_r_m Man page Source code
geneExprTest Man page Source code
getDesignMat Source code
initDat Man page Source code
loadERCCInfo Source code
loadExpMeas Source code
maSignal Man page Source code
normalizeDat Source code
plotAdjust Source code
prepERCCDat Source code
printLODRres Source code
runDashboard Man page Source code
saveERCCPlots Man page Source code
testDEArray Source code
testDECount Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/annotLODR.R
R/dashboardFile.R
R/dynRangePlot.R
R/erccROC.R
R/estLODR.R
R/est_r_m.R
R/geneExprTest.R
R/getDesignMat.R
R/initDat.R
R/loadERCCInfo.R
R/loadExpMeas.R
R/maSignal.R
R/normalizeDat.R
R/plotAdjust.R
R/prepERCCDat.R
R/printLODRres.R
R/runDashboard.R
R/saveERCCPlots.R
R/testDEArray.R
R/testDECount.R
build
build/vignette.rds
data
data/ERCC.RData
data/SEQC.Example.RData
data/datalist
inst
inst/CITATION
inst/doc
inst/doc/erccdashboard.R
inst/doc/erccdashboard.Rnw
inst/doc/erccdashboard.pdf
man
man/ERCC.Rd
man/ERCCDef.Rd
man/ERCCMix1and2.Rd
man/MET.CTL.countDat.Rd
man/MET.CTL.totalReads.Rd
man/SEQC.Example.Rd
man/UHRR.HBRR.arrayDat.Rd
man/UHRR.HBRR.countDat.Rd
man/UHRR.HBRR.totalReads.Rd
man/annotLODR.Rd
man/dynRangePlot.Rd
man/erccROC.Rd
man/estLODR.Rd
man/est_r_m.Rd
man/geneExprTest.Rd
man/initDat.Rd
man/maSignal.Rd
man/runDashboard.Rd
man/saveERCCPlots.Rd
vignettes
vignettes/erccdashboard.Rnw
erccdashboard documentation built on May 20, 2017, 10:22 p.m.