# NanoString GeoMx Tools

## Documentation for package ‘GeomxTools’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aggregateCounts | Aggregate probe counts to target level for feature data
checkQCFlags | Check QC Flags in the GeoMxSet and removes the probe or sample from the object
checkQCFlags-method | checkQCFlags
class:NanoStringGeoMxSet | Class to Contain NanoString Spatial Expression Level Assays
coerce-method | Class to Contain NanoString Spatial Expression Level Assays
countsShiftedByOne | Accessor to check if "exprs" 'assDataElement' was shifted by one
design-method | Class to Contain NanoString Spatial Expression Level Assays
design<--method | Class to Contain NanoString Spatial Expression Level Assays
dimLabels-method | Class to Contain NanoString Spatial Expression Level Assays
dimLabels<--method | Class to Contain NanoString Spatial Expression Level Assays
featureType | Class to Contain NanoString Spatial Expression Level Assays
featureType-method | Class to Contain NanoString Spatial Expression Level Assays
featureType<- | Class to Contain NanoString Spatial Expression Level Assays
featureType<--method | Class to Contain NanoString Spatial Expression Level Assays
logtBase | Get take the log of a numeric vector
mixedModelDE | Run a mixed model on GeoMxSet
NanoStringGeoMxSet | Class to Contain NanoString Spatial Expression Level Assays
NanoStringGeoMxSet-class | Class to Contain NanoString Spatial Expression Level Assays
NanoStringGeoMxSet-method | Class to Contain NanoString Spatial Expression Level Assays
ngeoMean | Get the geometric mean of a vector
ngeoSD | Get the geometric standard deviation of a vector
normalize-method | normalize
readDccFile | Read DCC File
readNanoStringGeoMxSet | Read 'NanoStringGeoMxSet'
readPKCFile | Read PKC File
sData | Class to Contain NanoString Spatial Expression Level Assays
sData-method | Class to Contain NanoString Spatial Expression Level Assays
setBackgroundQCFlags | Add background QC flags to NanoStringGeoMxSet object protocol data
setBioProbeQCFlags | Add probe QC flags to NanoStringGeoMxSet object feature data
setGeoMxQCFlags | Add GeoMx segment QC flags to NanoStringGeoMxSet object protocol data
setQCFlags-method | Add QC flags to feature and protocol data simultaneously
setSegmentQCFlags | Add segment QC flags to protocol data
setSeqQCFlags | Add sequencing QC flags to NanoStringGeoMxSet object protocol data
shiftCountsOne | Add one to all counts in an expression matrix
show-method | Class to Contain NanoString Spatial Expression Level Assays
signatureGroups | Class to Contain NanoString Spatial Expression Level Assays
signatureGroups-method | Class to Contain NanoString Spatial Expression Level Assays
signatures | Class to Contain NanoString Spatial Expression Level Assays
signatures-method | Class to Contain NanoString Spatial Expression Level Assays
signatures<- | Class to Contain NanoString Spatial Expression Level Assays
signatures<--method | Class to Contain NanoString Spatial Expression Level Assays
signatureScores | Class to Contain NanoString Spatial Expression Level Assays
signatureScores-method | Class to Contain NanoString Spatial Expression Level Assays
summarizeNegatives | Calculate negative probe summary stats
svarLabels | Class to Contain NanoString Spatial Expression Level Assays
svarLabels-method | Class to Contain NanoString Spatial Expression Level Assays
writeNanoStringGeoMxSet | write 'NanoStringGeoMxSet'