Package: standR 1.17.6

Ning Liu

standR: Spatial transcriptome analyses of Nanostring's DSP data in R

standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.

Authors:Ning Liu [aut, cre], Dharmesh D Bhuva [aut], Ahmed Mohamed [aut]

standR_1.17.6.tar.gz
standR_1.17.6.zip(r-4.7-any)standR_1.17.6.zip(r-4.6-any)standR_1.17.6.zip(r-4.5-any)
standR_1.17.6.tgz(r-4.6-any)standR_1.17.6.tgz(r-4.5-any)
standR_1.17.6.tar.gz(r-4.7-any)standR_1.17.6.tar.gz(r-4.6-any)
standR_1.17.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
standR/json (API)

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

Bug tracker:https://github.com/davislaboratory/standr/issues

On BioConductor:standR-1.17.5(bioc 3.24)standR-1.16.0(bioc 3.23)

spatialtranscriptomicsgeneexpressiondifferentialexpressionqualitycontrolnormalizationexperimenthubsoftware

7.01 score 27 stars 1 packages 72 scripts 675 downloads 23 exports 133 dependencies

Last updated from:06b50667f2. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE185
linux-develWARNING443
source / vignettesERROR290
linux-releaseWARNING443
macos-releaseWARNING253
macos-oldrelWARNING274
windows-develWARNING314
windows-releaseWARNING317
windows-oldrelWARNING250
wasm-releaseOK184

Exports:addPerROIQCcomputeClusterEvalStatsdrawPCAfindBestKfindNCGsgeomxBatchCorrectiongeomxNormplotClusterEvalStatsplotDRplotGeneQCplotMDSplotPairPCAplotPCAbiplotplotRLExprplotROIQCplotSampleInfoplotScreePCAprepareSpatialDeconreadGeoMxreadGeoMxFromDccreadGeoMxFromDGEreadGeoMxFromNanoStringGeoMxSetspe2dge

Dependencies:abindAnnotationDbiaroma.lightaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicliprcodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdigestdplyrEDASeqedgeRfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggalluvialggplot2gluegridExtragtablehmshttrhttr2hwriterinterpIRangesisobandjpegjsonliteKEGGRESTlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmamagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustcompmemoisemimeopensslpatchworkpillarpkgconfigpngprettyunitsprogresspurrrpwalignR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerruvRUVSeqS4ArraysS4VectorsS7scalesSeqinfoShortReadSingleCellExperimentsnowSparseArraySpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXMLxml2XVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Add QC statistics to the Spatial Experiment objectaddPerROIQC
Calculate statistics for evaluating batch correctioncomputeClusterEvalStats
Compute and plot the results of a PCA analysis on gene expression datadrawPCA drawPCA,DGEList-method drawPCA,ExpressionSet-method drawPCA,SingleCellExperiment-method drawPCA,SpatialExperiment-method drawPCA,SummarizedExperiment-method
Testing multiple K for RUV4 batch correction to find the best K.findBestK
Get negative control genes from each batch of the datafindNCGs
Batch correction for GeoMX datageomxBatchCorrection
Perform normalization to GeoMX datageomxNorm
Compare and evaluate different batch corrected data with plotting.plotClusterEvalStats
Compute and plot the results of any dimension reduction methods on gene expression dataplotDR plotDR,SingleCellExperiment-method plotDR,SpatialExperiment-method
Plot gene-wise QC plotplotGeneQC
Compute and plot the results of a MDS analysis on gene expression dataplotMDS plotMDS,DGEList-method plotMDS,ExpressionSet-method plotMDS,SingleCellExperiment-method plotMDS,SpatialExperiment-method plotMDS,SummarizedExperiment-method
Plot pair-wise PCA plots for multiple dimensionsplotPairPCA
Plot PCA bi plotplotPCAbiplot
Compute and plot relative log expression (RLE) values of gene expression dataplotRLExpr plotRLExpr,DGEList-method plotRLExpr,ExpressionSet-method plotRLExpr,SummarizedExperiment-method
Plot Sample-wise QC plotplotROIQC
Plot the user-defined meta data using alluvium plotplotSampleInfo
Plot the PCA scree plot.plotScreePCA
Prepare expression and background matrices for SpatialDeconprepareSpatialDecon
Import GeoMX DSP data into a saptial experiment object from file pathsreadGeoMx
Import GeoMX DSP data from DCC filesreadGeoMxFromDcc
Import GeoMX DSP data into a spatial experiment object from DGEList objectreadGeoMxFromDGE
Import GeoMX DSP data from a NanoStringGeoMxSet-like objectreadGeoMxFromNanoStringGeoMxSet
Transfer SpatialExperiment object into DGEList object for DE analysisspe2dge