Man pages for Nanostring-Biostats/GeomxTools
NanoString GeoMx Tools
| aggregateCounts | Aggregate probe counts to target level for feature data |
| as.Seurat | Convert GeoMxSet Object to SeuratObject |
| as.SpatialExperiment | Convert Object to SpatialExperiment |
| checkQCFlags | Check QC Flags in the GeoMxSet and removes the probe or... |
| checkQCFlags-NanoStringGeoMxSet-method | checkQCFlags |
| compareToConfig | Compare given PKC probes to probes in config file |
| computeNormalizationFactors | Generate normalization factors |
| countsShiftedByOne | Accessor to check if "exprs" 'assDataElement' was shifted by... |
| hkNames | Return the House Keeper positive controls for protein |
| iggNames | Return the IgG negative controls for protein |
| logtBase | Get take the log of a numeric vector |
| mixedModelDE | Run a mixed model on GeoMxSet |
| NanoStringGeoMxSet-class | 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-NanoStringGeoMxSet-method | normalize |
| plotConcordance | Generate concordance figure of targets based on user provided... |
| plotNormFactorConcordance | Generate concordance figure of normalization factors based on... |
| qcProteinSignal | Generate Protein QC signal boxplot figure |
| qcProteinSignalNames | Generate list of proteins ordered by SNR |
| readDccFile | Read DCC File |
| readNanoStringGeoMxSet | Read 'NanoStringGeoMxSet' |
| readPKCFile | Read PKC File |
| setBackgroundQCFlags | Add background QC flags to NanoStringGeoMxSet object protocol... |
| setBioProbeQCFlags | Add probe QC flags to NanoStringGeoMxSet object feature data |
| setGeoMxQCFlags | Add GeoMx segment QC flags to NanoStringGeoMxSet object... |
| setQCFlags-NanoStringGeoMxSet-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... |
| shiftCountsOne | Add one to all counts in an expression matrix |
| summarizeNegatives | Calculate negative probe summary stats |
| updateGeoMxSet | Update GeoMxSet object to current version |
| writeNanoStringGeoMxSet | write 'NanoStringGeoMxSet' |
