Package: RegionalST 1.11.0

Ziyi Li

RegionalST: Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

Authors:Ziyi Li [aut, cre]

RegionalST_1.11.0.tar.gz
RegionalST_1.11.0.zip(r-4.7)RegionalST_1.11.0.zip(r-4.6)RegionalST_1.11.0.zip(r-4.5)
RegionalST_1.11.0.tgz(r-4.6-any)RegionalST_1.11.0.tgz(r-4.5-any)
RegionalST_1.11.0.tar.gz(r-4.7-any)RegionalST_1.11.0.tar.gz(r-4.6-any)
RegionalST_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RegionalST/json (API)

# Install 'RegionalST' in R:

install.packages('RegionalST', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

example_sce - Example single cell experiment for input
exampleRes - Example DE output
pathways_hallmark - Hallmark database
pathways_kegg - KEGG database
pathways_reactome - REACTOME database

On BioConductor:RegionalST-1.11.0(bioc 3.24)RegionalST-1.10.0(bioc 3.23)

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

spatial transcriptomics reactome kegg

4.18 score 9 scripts 16 exports 247 dependencies

Last updated from:4e80d08f2c. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	238
linux-devel-x86_64	WARNING	458
source / vignettes	OK	353
linux-release-x86_64	WARNING	434
macos-release-arm64	WARNING	246
macos-oldrel-arm64	WARNING	283
windows-devel	WARNING	302
windows-release	WARNING	362
windows-oldrel	WARNING	306
wasm-release	OK	186

Exports:DoGSEA DrawDotplot DrawRegionProportion DrawRegionProportion_withProp FindRegionalCells GetCellTypeSpecificDE_withProp GetCrossRegionalDE_raw GetCrossRegionalDE_withProp GetOneRadiusEntropy GetOneRadiusEntropy_withProp getProportion ManualSelectCenter mySpatialPreprocess PlotOneSelectedCenter RankCenterByEntropy RankCenterByEntropy_withProp

Dependencies:abind annotate AnnotationDbi arrow askpass assertthat assorthead base64enc BayesSpace beachmat beeswarm BH Biobase BiocFileCache BiocGenerics biocmake BiocManager BiocNeighbors BiocParallel BiocSingular BiocStyle Biostrings bit bit64 bitops blob bluster bookdown bslib cachem Cairo caTools class cli cluster coda codetools colorspace commonmark corpcor cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir digest dir.expiry DirichletReg doParallel dotCall64 dplyr dqrng e1071 edgeR EpiDISH evaluate farver fastDummies fastmap fastmatch fgsea filelock fitdistrplus FNN fontawesome forcats foreach formatR Formula fs futile.logger futile.options future future.apply genefilter generics GenomicRanges GGally ggbeeswarm ggplot2 ggrastr ggrepel ggridges ggstats globals glue goftest gplots gridExtra gtable gtools here highr hms htmltools htmlwidgets httpuv httr httr2 ica igraph IRanges irlba isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma listenv lmtest locfdr locfit magrittr MASS Matrix MatrixGenerics matrixStats maxLik mclust memoise metapod microbenchmark mime miniUI miscTools nlme nnls openssl otel parallelly patchwork pbapply pheatmap pillar pkgconfig plotly plyr png polyclip prettyunits progress progressr promises proxy purrr quadprog R6 ragg RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppDist RcppEigen RcppHNSW RcppML RcppProgress RcppTOML RCurl reshape2 reticulate rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown ROCR rprojroot RSpectra RSQLite rsvd Rtsne S4Arrays S4Vectors S7 sandwich sass ScaledMatrix scales scater scattermore scran sctransform scuttle Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr SummarizedExperiment survival sys systemfonts tensor textshaping tibble tidyr tidyselect tinytex TOAST utf8 uwot vctrs vipor viridis viridisLite withr xfun xgboost XML xtable XVector yaml zoo

Understanding Intrasample Heterogeneity from ST data with RegionalST

Install RegionalST | Preparing your data for RegionalST through BayesSpace | Analysis with the incorporation of cell type proportions | Obtain cell deconvolution proportions | Load example dataset | Identify Regions of Interest (ROIs) with incorporation of proportions | Automatic ROI selection | Manual ROI selection | Draw cell type proportions for the selected ROIs | Perform Cross-regional Differential Analysis with proportions | Perform Cross-regional Cell Type-Specific Differential Analysis with proportions and self-defined regions | Analysis with cell type information | Obtain cell type labels | Identify Regions of Interest (ROIs) with cell type information | Automatic selection of the ROIs | Manual ROI selection with cell type information | Perform Cross-regional Differential Analysis with cell type information | Pathway GSEA analysis based on the cross-regional DEs | Session info

Rendered fromRegionalST.Rmdusingknitr::rmarkdown

Last update: 2024-11-11
Started: 2023-05-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Perform GSEA analysis for cross-regional DE genes	DoGSEA
Draw dot plot for GSEA results of cross-regional DE genes	DrawDotplot
Draw regional cell type distribution with cell type annotation information	DrawRegionProportion
Draw regional cell type distribution with cellular proportion information	DrawRegionProportion_withProp
Example single cell experiment for input	example_sce
Example DE output	exampleRes
Identify regional cells given centers and radiuses	FindRegionalCells
Identify cross-regional cell type-specific differential analysis with proportion	GetCellTypeSpecificDE_withProp
Identify cross-regional differential analysis	GetCrossRegionalDE_raw
Identify cross-regional differential analysis with proportion	GetCrossRegionalDE_withProp
Computer the entropy for a fixed radius	GetOneRadiusEntropy
Computer the entropy for a fixed radius with cell type proportion	GetOneRadiusEntropy_withProp
Define an accessor method for Proportion_CARD	getProportion
Manually select top ROIs	ManualSelectCenter
Perform Preprocessing for spatial data (tailored from BayesSpace function)	mySpatialPreprocess
Hallmark database	pathways_hallmark
KEGG database	pathways_kegg
REACTOME database	pathways_reactome
Plot one selected ROI	PlotOneSelectedCenter
Automatically rank ROI centers based on entropy	RankCenterByEntropy
Automatically rank ROI centers based on entropy with proportions	RankCenterByEntropy_withProp