API for Nanostring-Biostats/GeomxTools
NanoString GeoMx Tools

Global functions
.allFALSE	Source code
.allNA	Source code
.allTRUE	Source code
.allZero	Source code
.validDccSchema	Source code
.validNonNegativeInteger	Source code
.validNonNegativeNumber	Source code
.validPositiveNumber	Source code
NanoStringGeoMxSet	Man page
NanoStringGeoMxSet,ExpressionSet-method	Man page
NanoStringGeoMxSet,NanoStringGeoMxSet-method	Man page
NanoStringGeoMxSet,environment-method	Man page
NanoStringGeoMxSet,matrix-method	Man page
NanoStringGeoMxSet,missing-method	Man page
NanoStringGeoMxSet-class	Man page
aggregateCounts	Man page Source code
analyte	Man page
analyte,NanoStringGeoMxSet-method	Man page
appendFeatureFlags	Source code
appendSampleFlags	Source code
as.Seurat	Man page
as.Seurat.NanoStringGeoMxSet	Man page Source code
as.SpatialExperiment	Man page Source code
as.SpatialExperiment.NanoStringGeoMxSet	Man page Source code
changeLocalsToNA	Source code
checkCutoffs	Source code
checkQCFlags	Man page
checkQCFlags,NanoStringGeoMxSet-method	Man page
class:NanoStringGeoMxSet	Man page
coerce,ExpressionSet,NanoStringGeoMxSet-method	Man page
collapseCounts	Source code
compareToConfig	Man page Source code
computeNormalizationFactors	Man page Source code
concordancePlot	Source code
countsShiftedByOne	Man page Source code
design,NanoStringGeoMxSet-method	Man page
design<-,NanoStringGeoMxSet,ANY-method	Man page
design<-,NanoStringGeoMxSet,NULL-method	Man page
design<-,NanoStringGeoMxSet,formula-method	Man page
dimLabels,NanoStringGeoMxSet-method	Man page
dimLabels<-,NanoStringGeoMxSet,character-method	Man page
extract_pkc_modules	Source code
extract_pkc_names	Source code
extract_pkc_versions	Source code
featureType	Man page
featureType,NanoStringGeoMxSet-method	Man page
featureType<-	Man page
featureType<-,NanoStringGeoMxSet,character-method	Man page
generate_pkc_lookup	Source code
generate_pkc_targ_notes	Source code
hkNames	Man page Source code
hkNorm	Source code
iggNames	Man page Source code
logtBase	Man page Source code
mixedModelDE	Man page Source code
negNorm	Source code
ngeoMean	Man page Source code
ngeoSD	Man page Source code
normalize,NanoStringGeoMxSet-method	Man page
pgrubbs	Source code
plotConcordance	Man page Source code
plotNormFactorConcordance	Man page Source code
print.sd.log.ratio	Source code
qcProteinSignal	Man page Source code
qcProteinSignalNames	Man page Source code
qgrubbs	Source code
quantileNorm	Source code
readDccFile	Man page Source code
readNanoStringGeoMxSet	Man page Source code
readPKCFile	Man page Source code
removeFlagProbes	Source code
sData	Man page
sData,NanoStringGeoMxSet-method	Man page
setAlignedFlags	Source code
setAreaFlags	Source code
setBackgroundQCFlags	Man page Source code
setBioProbeQCFlags	Man page Source code
setGeoMxQCFlags	Man page Source code
setGrubbsFlags	Source code
setHighCountFlags	Source code
setHighNTCFlags	Source code
setLOQFlags	Source code
setLowNegFlags	Source code
setLowReadFlags	Source code
setNucleiFlags	Source code
setProbeCountFlags	Source code
setProbeRatioFlags	Source code
setQCFlags,NanoStringGeoMxSet-method	Man page
setSaturationFlags	Source code
setSegmentQCFlags	Man page Source code
setSeqQCFlags	Man page Source code
setStitchedFlags	Source code
setTargetFlags	Source code
setTrimmedFlags	Source code
shiftCountsOne	Man page Source code
show,NanoStringGeoMxSet-method	Man page
signatureGroups	Man page
signatureGroups,NanoStringGeoMxSet-method	Man page
signatureScores	Man page
signatureScores,NanoStringGeoMxSet-method	Man page
signatures	Man page
signatures,NanoStringGeoMxSet-method	Man page
signatures<-	Man page
signatures<-,NanoStringGeoMxSet,SignatureSet-method	Man page
snrOrder	Source code
subtractBackground	Source code
summarizeNegatives	Man page Source code
svarLabels	Man page
svarLabels,NanoStringGeoMxSet-method	Man page
thresholdValues	Source code
updateGeoMxSet	Man page Source code
updateObject,NanoStringGeoMxSet-method	Man page
writeNanoStringGeoMxSet	Man page Source code