NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data

NanoStringQCPro provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data -- i.e. to identify outlier probes and outlier samples. It also provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and an easily sharable html quality control output.

AuthorDorothee Nickles <nickles.dorothee@gene.com>, Thomas Sandmann <sandmann.thomas@gene.com>, Robert Ziman <ziman.robert@gene.com>, Richard Bourgon <bourgon.richard@gene.com>
Date of publicationNone
MaintainerRobert Ziman <ziman.robert@gene.com>
LicenseArtistic-2.0
Version1.6.0

View on Bioconductor

Man pages

addCodesetAnnotation: Add NanoString codeset annotation to an RccSet

addQCFlags: Add sample QC flags to an rccSet

allSumPlot: allSumPlot

assessHousekeeping: assessHousekeeping

bdPlot: Binding density plot

buildCodesetAnnotation: Build NanoString codeset annotation

checkRccSet: Check an RccSet

colByCovar: colByCovar

colByFun: colByFun

contentNorm: Content normalization

copyRccSet: Deep-copy a NanoString RccSet

countsInBlankSamples_verticalPlot: Plot counts in blank samples (vertical orientation)

ctrlsOverviewPlot: ctrlsOverviewPlot

ctrlsZprimePlot: ctrlsZprimePlot

cutoffByMMAD: cutoffByMMAD

cutoffByVar: cutoffByVar

dCoVar: dCoVar

densityPlot: densityPlot

example_rccSet: NanoStringQCPro example dataset

flagSamplesCount: flagSamplesCount

flagSamplesCtrl: flagSamplesCtrl

flagSamplesTech: flagSamplesTech

fovPlot: Fields of view (FOV) plot

geneClustering: Gene clustering heatmap

getBackground: Get background estimates for a NanoString RccSet

getBlankLabel: Get the SampleType value that indicates blank samples

getSpikeInInput: getSpikeInInput

iqrPlot: iqrPlot

lodAssess: lodAssess

lodPlot: lodPlot

makeQCReport: Make NanoString QC report

myCols: myCols

NanoStringQCPro: NanoStringQCPro

negCtrlsByLane: negCtrlsByLane

negCtrlsByLane_verticalPlot: Plot of negative controls by lane (vertical orientation)

negCtrlsPairs: negCtrlsPairs

negCtrlsPlot: negCtrlsPlot

newRccSet: Create a new RccSet object

nSolverBackground: nSolver Analysis Software background estimation

nSolverCsv.to.pdata_fdata_adata: nSolverCsv.to.pdata_fdata_fdata

panelCor: panelCor

pcaPlot: pcaPlot

pdata_fdata_adata.to.rccSet: pdata_fdata_adata.to.rccSet

posCtrlNorm: Positive control normalization

posNormFactPlot: posNormFactPlot

posR2Plot: posR2Plot

posRatioPlot: posRatioPlot

posSlopePlot: posSlopePlot

posSumVsAllSumPlot: posSumVsAllSumPlot

preprocRccSet: Preprocess an RccSet

presAbsCall: Presence/absence call

previewPNG: Create a preview of a PNG

rccFiles.to.pdata_fdata_adata: rccFiles.to.pdata_fdata_adata

RccSet: RccSet constructor methods

RccSet-class: RccSet class, derived from ExpressionSet

readCdrDesignData: Read .CSV containing CDR 'Design Data' extract

readRcc: Read an .RCC file

readRccBatch: Read RCC files

readRccCollectorToolExport: Read RCC Collector Tool Export

readRlf: Read RLF file

sampleClustering: Clustering by sample correlation

scatterPair: scatterPair

subtractBackground: Subtract background estimates for a NanoString RccSet

zfacFun: zfacFun

Functions

addCodesetAnnotation Man page
addCodesetAnnotation,RccSet-method Man page
addQCFlags Man page
addQCFlags,RccSet-method Man page
allSumPlot Man page
allSumPlot,RccSet-method Man page
assessHousekeeping Man page
assessHousekeeping,RccSet-method Man page
bdPlot Man page
bdPlot,RccSet-method Man page
buildCodesetAnnotation Man page
checkRccSet Man page
checkRccSet,RccSet-method Man page
colByCovar Man page
colByFun Man page
contentNorm Man page
contentNorm,RccSet-method Man page
copyRccSet Man page
copyRccSet,RccSet-method Man page
countsInBlankSamples_verticalPlot Man page
ctrlsOverviewPlot Man page
ctrlsOverviewPlot,RccSet-method Man page
ctrlsZprimePlot Man page
ctrlsZprimePlot,RccSet-method Man page
cutoffByMMAD Man page
cutoffByVar Man page
dCoVar Man page
densityPlot Man page
example_rccSet Man page
flagSamplesCount Man page
flagSamplesCount,RccSet-method Man page
flagSamplesCtrl Man page
flagSamplesCtrl,RccSet-method Man page
flagSamplesTech Man page
flagSamplesTech,RccSet-method Man page
fovPlot Man page
fovPlot,RccSet-method Man page
geneClustering Man page
getBackground Man page
getBackground,RccSet-method Man page
getBlankLabel Man page
getBlankLabel,RccSet-method Man page
getSpikeInInput Man page
iqrPlot Man page
iqrPlot,RccSet-method Man page
lodAssess Man page
lodAssess,RccSet-method Man page
lodPlot Man page
lodPlot,RccSet-method Man page
makeQCReport Man page
makeQCReport,RccSet-method Man page
myCols Man page
NanoStringQCPro Man page
NanoStringQCPro-package Man page
negCtrlsByLane Man page
negCtrlsByLane,RccSet-method Man page
negCtrlsByLane_verticalPlot Man page
negCtrlsPairs Man page
negCtrlsPairs,RccSet-method Man page
negCtrlsPlot Man page
negCtrlsPlot,RccSet-method Man page
newRccSet Man page
nSolverBackground Man page
nSolverBackground,RccSet-method Man page
nSolverCsv.to.pdata_fdata_adata Man page
panelCor Man page
pcaPlot Man page
pdata_fdata_adata.to.rccSet Man page
posCtrlNorm Man page
posCtrlNorm,RccSet-method Man page
posNormFactPlot Man page
posNormFactPlot,RccSet-method Man page
posR2Plot Man page
posR2Plot,RccSet-method Man page
posRatioPlot Man page
posRatioPlot,RccSet-method Man page
posSlopePlot Man page
posSlopePlot,RccSet-method Man page
posSumVsAllSumPlot Man page
posSumVsAllSumPlot,RccSet-method Man page
preprocRccSet Man page
preprocRccSet,RccSet-method Man page
presAbsCall Man page
presAbsCall,RccSet-method Man page
previewPNG Man page
rccFiles.to.pdata_fdata_adata Man page
RccSet Man page
.RccSet Man page
RccSet-class Man page
RccSet,environment-method Man page
RccSet,ExpressionSet-method Man page
RccSet,matrix-method Man page
RccSet,missing-method Man page
readCdrDesignData Man page
readRcc Man page
readRccBatch Man page
readRccCollectorToolExport Man page
readRlf Man page
sampleClustering Man page
sampleClustering,RccSet-method Man page
scatterPair Man page
subtractBackground Man page
subtractBackground,RccSet-method Man page
zfacFun Man page

Files

NanoStringQCPro/DESCRIPTION
NanoStringQCPro/NAMESPACE
NanoStringQCPro/R
NanoStringQCPro/R/0_RccSet-class.R NanoStringQCPro/R/BackgroundSubtractionFunctions.R NanoStringQCPro/R/NanoStringConvenience.R
NanoStringQCPro/R/NanoStringQCPro-package.r
NanoStringQCPro/R/NanoStringQCreport.R NanoStringQCPro/R/NanoStringQualityMetrics.R NanoStringQCPro/R/example_rccSet.R NanoStringQCPro/R/previewPNG.R NanoStringQCPro/R/utils.R
NanoStringQCPro/build
NanoStringQCPro/build/vignette.rds
NanoStringQCPro/data
NanoStringQCPro/data/example_rccSet.rdata
NanoStringQCPro/inst
NanoStringQCPro/inst/NEWS.Rd
NanoStringQCPro/inst/doc
NanoStringQCPro/inst/doc/vignetteNanoStringQCPro.R
NanoStringQCPro/inst/doc/vignetteNanoStringQCPro.Rnw
NanoStringQCPro/inst/doc/vignetteNanoStringQCPro.pdf
NanoStringQCPro/inst/examples
NanoStringQCPro/inst/examples/main.R
NanoStringQCPro/inst/extdata
NanoStringQCPro/inst/extdata/CDR
NanoStringQCPro/inst/extdata/CDR/CDR-DesignData.csv
NanoStringQCPro/inst/extdata/RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C1-unstim_C1-unstim_01.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C1-unstim_C1-unstim_03.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C1-unstim_C1-unstim_04.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C1-unstim_C1-unstim_05.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C1-unstim_C1-unstim_08.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C1-unstim_C1-unstim_12.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C2-unstim_C2-unstim_02.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C2-unstim_C2-unstim_04.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C2-unstim_C2-unstim_06.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C2-unstim_C2-unstim_10.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C2-unstim_C2-unstim_10_2.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C2-unstim_C2-unstim_11.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C2-unstim_C2-unstim_12.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C3-stim_C3-stim_01.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C3-stim_C3-stim_02.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C3-stim_C3-stim_04.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C3-stim_C3-stim_07.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C3-stim_C3-stim_09.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C3-stim_C3-stim_11.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C4-stim_C4-stim_03.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C4-stim_C4-stim_04.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C4-stim_C4-stim_06.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C4-stim_C4-stim_07.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C4-stim_C4-stim_10.RCC
NanoStringQCPro/inst/extdata/RCC/20140604_C4-stim_C4-stim_12.RCC
NanoStringQCPro/inst/extdata/RLF
NanoStringQCPro/inst/extdata/RLF/NQCP_example.rlf
NanoStringQCPro/inst/extdata/extraPdata
NanoStringQCPro/inst/extdata/extraPdata/SampleType.txt
NanoStringQCPro/inst/extdata/nSolver
NanoStringQCPro/inst/extdata/nSolver/RCC_collector_tool_export.csv
NanoStringQCPro/inst/misc
NanoStringQCPro/inst/misc/qcReportHeader.html
NanoStringQCPro/inst/templates
NanoStringQCPro/inst/templates/QualityControlReportTemplate.Rmd
NanoStringQCPro/man
NanoStringQCPro/man/NanoStringQCPro.Rd NanoStringQCPro/man/RccSet-class.Rd NanoStringQCPro/man/RccSet.Rd NanoStringQCPro/man/addCodesetAnnotation.Rd NanoStringQCPro/man/addQCFlags.Rd NanoStringQCPro/man/allSumPlot.Rd NanoStringQCPro/man/assessHousekeeping.Rd NanoStringQCPro/man/bdPlot.Rd NanoStringQCPro/man/buildCodesetAnnotation.Rd NanoStringQCPro/man/checkRccSet.Rd NanoStringQCPro/man/colByCovar.Rd NanoStringQCPro/man/colByFun.Rd NanoStringQCPro/man/contentNorm.Rd NanoStringQCPro/man/copyRccSet.Rd NanoStringQCPro/man/countsInBlankSamples_verticalPlot.Rd NanoStringQCPro/man/ctrlsOverviewPlot.Rd NanoStringQCPro/man/ctrlsZprimePlot.Rd NanoStringQCPro/man/cutoffByMMAD.Rd NanoStringQCPro/man/cutoffByVar.Rd NanoStringQCPro/man/dCoVar.Rd NanoStringQCPro/man/densityPlot.Rd NanoStringQCPro/man/example_rccSet.Rd NanoStringQCPro/man/flagSamplesCount.Rd NanoStringQCPro/man/flagSamplesCtrl.Rd NanoStringQCPro/man/flagSamplesTech.Rd NanoStringQCPro/man/fovPlot.Rd NanoStringQCPro/man/geneClustering.Rd NanoStringQCPro/man/getBackground.Rd NanoStringQCPro/man/getBlankLabel.Rd NanoStringQCPro/man/getSpikeInInput.Rd NanoStringQCPro/man/iqrPlot.Rd NanoStringQCPro/man/lodAssess.Rd NanoStringQCPro/man/lodPlot.Rd NanoStringQCPro/man/makeQCReport.Rd NanoStringQCPro/man/myCols.Rd NanoStringQCPro/man/nSolverBackground.Rd NanoStringQCPro/man/nSolverCsv.to.pdata_fdata_adata.Rd NanoStringQCPro/man/negCtrlsByLane.Rd NanoStringQCPro/man/negCtrlsByLane_verticalPlot.Rd NanoStringQCPro/man/negCtrlsPairs.Rd NanoStringQCPro/man/negCtrlsPlot.Rd NanoStringQCPro/man/newRccSet.Rd NanoStringQCPro/man/panelCor.Rd NanoStringQCPro/man/pcaPlot.Rd NanoStringQCPro/man/pdata_fdata_adata.to.rccSet.Rd NanoStringQCPro/man/posCtrlNorm.Rd NanoStringQCPro/man/posNormFactPlot.Rd NanoStringQCPro/man/posR2Plot.Rd NanoStringQCPro/man/posRatioPlot.Rd NanoStringQCPro/man/posSlopePlot.Rd NanoStringQCPro/man/posSumVsAllSumPlot.Rd NanoStringQCPro/man/preprocRccSet.Rd NanoStringQCPro/man/presAbsCall.Rd NanoStringQCPro/man/previewPNG.Rd NanoStringQCPro/man/rccFiles.to.pdata_fdata_adata.Rd NanoStringQCPro/man/readCdrDesignData.Rd NanoStringQCPro/man/readRcc.Rd NanoStringQCPro/man/readRccBatch.Rd NanoStringQCPro/man/readRccCollectorToolExport.Rd NanoStringQCPro/man/readRlf.Rd NanoStringQCPro/man/sampleClustering.Rd NanoStringQCPro/man/scatterPair.Rd NanoStringQCPro/man/subtractBackground.Rd NanoStringQCPro/man/zfacFun.Rd
NanoStringQCPro/vignettes
NanoStringQCPro/vignettes/NanoStringQCProOverview.pdf
NanoStringQCPro/vignettes/vignetteNanoStringQCPro.Rnw

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