Package: standR 1.11.1

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_1.11.1.tar.gz
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standR_1.11.1.tgz(r-4.4-any)standR_1.11.1.tgz(r-4.3-any)
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standR.pdf |standR.html✨
standR/json (API)
NEWS

# 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-1.11.1(bioc 3.21)standR-1.10.0(bioc 3.20)

spatial transcriptomics geneexpression differentialexpression qualitycontrol normalization experimenthubsoftware

7.37 score 18 stars 41 scripts 268 downloads 21 exports 141 dependencies

Last updated 2 months agofrom:0dbb86e18c. Checks:7 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 03 2025
R-4.5-win	OK	Jan 03 2025
R-4.5-linux	OK	Jan 03 2025
R-4.4-win	OK	Jan 03 2025
R-4.4-mac	OK	Jan 03 2025
R-4.3-win	OK	Jan 03 2025
R-4.3-mac	OK	Jan 03 2025

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

Dependencies:abind AnnotationDbi aroma.light askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cli clipr codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray deldir digest dplyr EDASeq edgeR fansi farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 mgcv mime munsell nlme openssl patchwork pillar pkgconfig plogr 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 scales ShortRead SingleCellExperiment snow SparseArray SpatialExperiment statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 XVector yaml zlibbioc

A quick start guide to the standR package

Ning Liu, Dharmesh Bhuva, Ahmed Mohamed, Chin Wee Tan, Melissa Davis

Rendered fromQuick_start.Rmdusingknitr::rmarkdownon Jan 03 2025.

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
Transfer SpatialExperiment object into DGEList object for DE analysis	spe2dge