Package: GeomxTools 3.11.0

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:Maddy Griswold [cre, aut], Nicole Ortogero [aut], Zhi Yang [aut], Ronalyn Vitancol [aut], David Henderson [aut]

GeomxTools_3.11.0.tar.gz
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GeomxTools.pdf |GeomxTools.html✨
GeomxTools/json (API)
NEWS

# Install 'GeomxTools' in R:
install.packages('GeomxTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:GeomxTools-3.9.1(bioc 3.20)GeomxTools-3.8.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseqsequencingexperimentaldesignnormalizationspatial

7.25 score 3 packages 189 scripts 748 downloads 44 exports 118 dependencies

Last updated 23 days agofrom:d685805e3a. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macERROROct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:aggregateCountsanalyteas.Seuratas.SpatialExperimentcheckQCFlagscomputeNormalizationFactorscountsShiftedByOnedesigndesign<-dimLabelsdimLabels<-featureTypefeatureType<-hkNamesiggNameslogtBasemixedModelDENanoStringGeoMxSetngeoMeanngeoSDnormalizeplotConcordanceplotNormFactorConcordanceqcProteinSignalqcProteinSignalNamesreadDccFilereadNanoStringGeoMxSetreadPKCFilesDatasetBackgroundQCFlagssetBioProbeQCFlagssetGeoMxQCFlagssetSegmentQCFlagssetSeqQCFlagsshiftCountsOneshowsignatureGroupssignaturessignatures<-signatureScoressummarizeNegativessvarLabelsupdateGeoMxSetwriteNanoStringGeoMxSet

Dependencies:askpassbase64encbeeswarmBiobaseBiocGenericsBiostringsbootbslibcachemcellrangerclicodetoolscolorspacecpp11crayoncurldata.tabledigestdotCall64dplyrEnvStatsevaluatefansifarverfastmapfontawesomeforcatsfsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGGallyggbeeswarmggiraphggplot2ggstatsggthemesglobalsgluegtablehighrhmshtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclelistenvlme4lmerTestmagrittrMASSMatrixmemoisemgcvmimeminqamunsellNanoStringNCToolsnlmenloptrnortestnumDerivopensslparallellypatchworkpheatmappillarpkgconfigplyrprettyunitsprogressprogressrpurrrR6rappdirsRColorBrewerRcppRcppEigenreadxlrematchreshape2rjsonrlangrmarkdownS4VectorssassscalesSeuratObjectspspamstringistringrsyssystemfontstibbletidyrtidyselecttinytexUCSC.utilsutf8uuidvctrsviporviridisLitewithrxfunXVectoryamlzlibbioc

Coercion of GeoMxSet to Seurat and SpatialExperiment Objects

Rendered fromGeomxSet_coercions.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-03-28
Started: 2022-02-04

Developer Introduction to the NanoStringGeoMxSet

David Henderson, Patrick Aboyoun, Nicole Ortogero, Zhi Yang, Jason Reeves, Kara Gorman, Rona Vitancol, Thomas Smith, Maddy Griswold

Rendered fromDeveloper_Introduction_to_the_NanoStringGeoMxSet.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-04-11
Started: 2021-06-25

Protein data using GeomxTools

Rendered fromProtein_in_GeomxTools.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-02-09
Started: 2022-04-11

Readme and manuals

Help Manual

Help pageTopics
Aggregate probe counts to target level for feature dataaggregateCounts
Convert GeoMxSet Object to SeuratObjectas.Seurat as.Seurat.NanoStringGeoMxSet
Convert Object to SpatialExperimentas.SpatialExperiment as.SpatialExperiment.NanoStringGeoMxSet
Check QC Flags in the GeoMxSet and removes the probe or sample from the objectcheckQCFlags
checkQCFlagscheckQCFlags,NanoStringGeoMxSet-method
Compare given PKC probes to probes in config filecompareToConfig
Generate normalization factorscomputeNormalizationFactors
Accessor to check if "exprs" 'assDataElement' was shifted by onecountsShiftedByOne
Return the House Keeper positive controls for proteinhkNames
Return the IgG negative controls for proteiniggNames
Get take the log of a numeric vectorlogtBase
Run a mixed model on GeoMxSetmixedModelDE
Class to Contain NanoString Spatial Expression Level Assaysanalyte 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 vectorngeoMean
Get the geometric standard deviation of a vectorngeoSD
normalizenormalize,NanoStringGeoMxSet-method
Generate concordance figure of targets based on user provided factorsplotConcordance
Generate concordance figure of normalization factors based on user provided factorsplotNormFactorConcordance
Generate Protein QC signal boxplot figureqcProteinSignal
Generate list of proteins ordered by SNRqcProteinSignalNames
Read DCC FilereadDccFile
Read 'NanoStringGeoMxSet'readNanoStringGeoMxSet
Read PKC FilereadPKCFile
Add background QC flags to NanoStringGeoMxSet object protocol datasetBackgroundQCFlags
Add probe QC flags to NanoStringGeoMxSet object feature datasetBioProbeQCFlags
Add GeoMx segment QC flags to NanoStringGeoMxSet object protocol datasetGeoMxQCFlags
Add QC flags to feature and protocol data simultaneouslysetQCFlags,NanoStringGeoMxSet-method
Add segment QC flags to protocol datasetSegmentQCFlags
Add sequencing QC flags to NanoStringGeoMxSet object protocol datasetSeqQCFlags
Add one to all counts in an expression matrixshiftCountsOne
Calculate negative probe summary statssummarizeNegatives
Update GeoMxSet object to current versionupdateGeoMxSet
write 'NanoStringGeoMxSet'writeNanoStringGeoMxSet