Overview | Data Processing | Seurat | Seurat Coercion | Simple GeoMx data workflow | In-depth GeoMx data workflow | Spatial Graphing | SpatialExperiment | SpatialExperiment Coercion | Image Overlays
Package: GeomxTools 3.17.0
Maddy Griswold
GeomxTools: NanoString GeoMx Tools
Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.
Authors:
GeomxTools_3.17.0.tar.gz
GeomxTools_3.17.0.zip(r-4.7-any)GeomxTools_3.17.0.zip(r-4.6-any)GeomxTools_3.17.0.zip(r-4.5-any)
GeomxTools_3.17.0.tgz(r-4.6-any)GeomxTools_3.17.0.tgz(r-4.5-any)
GeomxTools_3.17.0.tar.gz(r-4.7-any)GeomxTools_3.17.0.tar.gz(r-4.6-any)
GeomxTools_3.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeomxTools/json (API)
| # Install 'GeomxTools' in R: |
| install.packages('GeomxTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:GeomxTools-3.17.0(bioc 3.24)GeomxTools-3.16.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseqsequencingexperimentaldesignnormalizationspatial
Last updated from:37ea8120ca. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 224 | ||
| linux-devel | NOTE | 960 | ||
| source / vignettes | OK | 426 | ||
| linux-release | NOTE | 968 | ||
| macos-release | NOTE | 789 | ||
| macos-oldrel | NOTE | 808 | ||
| windows-devel | NOTE | 909 | ||
| windows-release | NOTE | 1062 | ||
| windows-oldrel | NOTE | 820 | ||
| wasm-release | OK | 183 |
Exports:aggregateCountsanalyteas.Seuratas.SpatialExperimentcheckQCFlagscomputeNormalizationFactorscountsShiftedByOnedesigndesign<-dimLabelsdimLabels<-featureTypefeatureType<-hkNamesiggNameslogtBasemixedModelDENanoStringGeoMxSetngeoMeanngeoSDnormalizeplotConcordanceplotNormFactorConcordanceqcProteinSignalqcProteinSignalNamesreadDccFilereadNanoStringGeoMxSetreadPKCFilesDatasetBackgroundQCFlagssetBioProbeQCFlagssetGeoMxQCFlagssetSegmentQCFlagssetSeqQCFlagsshiftCountsOneshowsignatureGroupssignaturessignatures<-signatureScoressummarizeNegativessvarLabelsupdateGeoMxSetwriteNanoStringGeoMxSet
Dependencies:base64encbeeswarmBiobaseBiocGenericsBiostringsbootbslibcachemcellrangerclicodetoolscpp11crayondata.tabledigestdotCall64dplyrEnvStatsevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforcatsfsfuturefuture.applygdtoolsgenericsGGallyggbeeswarmggiraphggplot2ggstatsggthemesglobalsgluegtablehighrhmshtmltoolshtmlwidgetsIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclelistenvlme4lmerTestmagrittrMASSMatrixmemoisemimeminqaNanoStringNCToolsnlmenloptrnortestnumDerivparallellypatchworkpheatmappillarpkgconfigplyrprettyunitsprogressprogressrpurrrR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreadxlreformulasrematchreshape2rjsonrlangrmarkdownS4VectorsS7sassscalesSeqinfoSeuratObjectspspamstringistringrsystemfontstibbletidyrtidyselecttinytexutf8vctrsviporviridisLitewithrxfunXVectoryaml
Coercion of GeoMxSet to Seurat and SpatialExperiment Objects
Last update: 2025-09-12
Started: 2022-02-04
Protein data using GeomxTools
Overview | Data Processing | RNA | Protein | Segment QC | Target QC | Normalization
Last update: 2024-02-09
Started: 2022-04-11
Developer Introduction to the NanoStringGeoMxSet
Introduction | Loading Packages | Building a NanoStringGeoMxSet from .DCC files | How is the DSP data stored in the NanoStringGeoMxSet object? | Accessing and Assigning NanoStringGeoMxSet Data Members | Access annotations | Summarizing NanoString GeoMx Data | Subsetting NanoStringGeoMxSet Objects | Apply Functions Across Assay Data | Built-in Quality Control Assessment | Normalization | Transforming NanoStringRCCSet Data to Data Frames | Transforming NanoSetRccSet assayData matrices
Last update: 2022-04-11
Started: 2021-06-25
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregate probe counts to target level for feature data | aggregateCounts |
| Convert GeoMxSet Object to SeuratObject | as.Seurat as.Seurat.NanoStringGeoMxSet |
| Convert Object to SpatialExperiment | as.SpatialExperiment as.SpatialExperiment.NanoStringGeoMxSet |
| Check QC Flags in the GeoMxSet and removes the probe or sample from the object | checkQCFlags |
| checkQCFlags | checkQCFlags,NanoStringGeoMxSet-method |
| Compare given PKC probes to probes in config file | compareToConfig |
| Generate normalization factors | computeNormalizationFactors |
| Accessor to check if "exprs" 'assDataElement' was shifted by one | countsShiftedByOne |
| Return the House Keeper positive controls for protein | hkNames |
| Return the IgG negative controls for protein | iggNames |
| Get take the log of a numeric vector | logtBase |
| Run a mixed model on GeoMxSet | mixedModelDE |
| Class to Contain NanoString Spatial Expression Level Assays | analyte analyte,NanoStringGeoMxSet-method class:NanoStringGeoMxSet coerce,ExpressionSet,NanoStringGeoMxSet-method design,NanoStringGeoMxSet-method design<-,NanoStringGeoMxSet,ANY-method design<-,NanoStringGeoMxSet,formula-method design<-,NanoStringGeoMxSet,NULL-method dimLabels,NanoStringGeoMxSet-method dimLabels<-,NanoStringGeoMxSet,character-method featureType featureType,NanoStringGeoMxSet-method featureType<- featureType<-,NanoStringGeoMxSet,character-method NanoStringGeoMxSet NanoStringGeoMxSet,environment-method NanoStringGeoMxSet,ExpressionSet-method NanoStringGeoMxSet,matrix-method NanoStringGeoMxSet,missing-method NanoStringGeoMxSet,NanoStringGeoMxSet-method NanoStringGeoMxSet-class sData sData,NanoStringGeoMxSet-method show,NanoStringGeoMxSet-method signatureGroups signatureGroups,NanoStringGeoMxSet-method signatures signatures,NanoStringGeoMxSet-method signatures<- signatures<-,NanoStringGeoMxSet,SignatureSet-method signatureScores signatureScores,NanoStringGeoMxSet-method svarLabels svarLabels,NanoStringGeoMxSet-method updateObject,NanoStringGeoMxSet-method |
| Get the geometric mean of a vector | ngeoMean |
| Get the geometric standard deviation of a vector | ngeoSD |
| normalize | normalize,NanoStringGeoMxSet-method |
| Generate concordance figure of targets based on user provided factors | plotConcordance |
| Generate concordance figure of normalization factors based on user provided factors | plotNormFactorConcordance |
| Generate Protein QC signal boxplot figure | qcProteinSignal |
| Generate list of proteins ordered by SNR | qcProteinSignalNames |
| Read DCC File | readDccFile |
| Read 'NanoStringGeoMxSet' | readNanoStringGeoMxSet |
| Read PKC File | readPKCFile |
| Add background QC flags to NanoStringGeoMxSet object protocol data | setBackgroundQCFlags |
| Add probe QC flags to NanoStringGeoMxSet object feature data | setBioProbeQCFlags |
| Add GeoMx segment QC flags to NanoStringGeoMxSet object protocol data | setGeoMxQCFlags |
| Add QC flags to feature and protocol data simultaneously | setQCFlags,NanoStringGeoMxSet-method |
| Add segment QC flags to protocol data | setSegmentQCFlags |
| Add sequencing QC flags to NanoStringGeoMxSet object protocol data | setSeqQCFlags |
| Add one to all counts in an expression matrix | shiftCountsOne |
| Calculate negative probe summary stats | summarizeNegatives |
| Update GeoMxSet object to current version | updateGeoMxSet |
| write 'NanoStringGeoMxSet' | writeNanoStringGeoMxSet |