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

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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.

Author
Dorothee 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 publication
None
Maintainer
Robert Ziman <ziman.robert@gene.com>
License
Artistic-2.0
Version
1.6.0

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

Files in this package

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