Package: standR 1.17.2

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_1.17.2.tar.gz
standR_1.17.2.zip(r-4.7)standR_1.17.2.zip(r-4.6)standR_1.17.2.zip(r-4.5)
standR_1.17.2.tgz(r-4.6-any)standR_1.17.2.tgz(r-4.5-any)
standR_1.17.2.tar.gz(r-4.7-any)standR_1.17.2.tar.gz(r-4.6-any)
standR_1.17.2.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-1.17.0(bioc 3.24)standR-1.16.0(bioc 3.23)

spatial transcriptomics geneexpression differentialexpression qualitycontrol normalization experimenthubsoftware

7.82 score 25 stars 1 packages 63 scripts 22 exports 134 dependencies

Last updated from:8a8f1be64b. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	241
linux-devel-x86_64	NOTE	470
source / vignettes	OK	323
linux-release-x86_64	NOTE	432
macos-release-arm64	NOTE	259
macos-oldrel-arm64	NOTE	191
windows-devel	NOTE	333
windows-release	NOTE	355
windows-oldrel	NOTE	301
wasm-release	OK	441

Exports:addPerROIQC computeClusterEvalStats drawPCA findBestK findNCGs geomxBatchCorrection geomxNorm plotClusterEvalStats plotDR plotGeneQC plotMDS plotPairPCA plotPCAbiplot plotRLExpr plotROIQC plotSampleInfo plotScreePCA prepareSpatialDecon readGeoMx readGeoMxFromDGE readGeoMxFromNanoStringGeoMxSet spe2dge

Dependencies:abind AnnotationDbi aroma.light askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cigarillo cli clipr codetools cpp11 crayon curl DBI dbplyr DelayedArray deldir dplyr EDASeq edgeR farver fastmap filelock formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggalluvial ggplot2 glue gridExtra gtable hms httr httr2 hwriter interp IRanges isoband jpeg jsonlite KEGGREST labeling lambda.r lattice latticeExtra lazyeval lifecycle limma locfit magick magrittr MASS Matrix MatrixGenerics matrixStats mclustcomp memoise mime openssl patchwork pillar pkgconfig png prettyunits progress purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer ruv RUVSeq S4Arrays S4Vectors S7 scales Seqinfo ShortRead SingleCellExperiment snow SparseArray SpatialExperiment statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr XML xml2 XVector yaml

A quick start guide to the standR package

Rendered fromQuick_start.Rmdusingknitr::rmarkdown

Last update: 2023-03-29
Started: 2023-02-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add QC statistics to the Spatial Experiment object	addPerROIQC
Calculate statistics for evaluating batch correction	computeClusterEvalStats
Compute and plot the results of a PCA analysis on gene expression data	drawPCA 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 data	findNCGs
Batch correction for GeoMX data	geomxBatchCorrection
Perform normalization to GeoMX data	geomxNorm
Compare and evaluate different batch corrected data with plotting.	plotClusterEvalStats
Compute and plot the results of any dimension reduction methods on gene expression data	plotDR plotDR,SingleCellExperiment-method plotDR,SpatialExperiment-method
Plot gene-wise QC plot	plotGeneQC
Compute and plot the results of a MDS analysis on gene expression data	plotMDS plotMDS,DGEList-method plotMDS,ExpressionSet-method plotMDS,SingleCellExperiment-method plotMDS,SpatialExperiment-method plotMDS,SummarizedExperiment-method
Plot pair-wise PCA plots for multiple dimensions	plotPairPCA
Plot PCA bi plot	plotPCAbiplot
Compute and plot relative log expression (RLE) values of gene expression data	plotRLExpr plotRLExpr,DGEList-method plotRLExpr,ExpressionSet-method plotRLExpr,SummarizedExperiment-method
Plot Sample-wise QC plot	plotROIQC
Plot the user-defined meta data using alluvium plot	plotSampleInfo
Plot the PCA scree plot.	plotScreePCA
Preparing the inputs for SpatialDecon for doing deconvolution on spatial data	prepareSpatialDecon
Import GeoMX DSP data into a saptial experiment object from file paths	readGeoMx
Import GeoMX DSP data into a spatial experiment object from DGEList object	readGeoMxFromDGE
Import GeoMX DSP data from a NanoStringGeoMxSet-like object	readGeoMxFromNanoStringGeoMxSet
Transfer SpatialExperiment object into DGEList object for DE analysis	spe2dge