Package: scider 1.3.0

Yunshun Chen

scider: Spatial cell-type inter-correlation by density in R

scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

Authors:Ning Liu [aut], Mengbo Li [aut], Yunshun Chen [aut, cre]

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scider.pdf |scider.html✨
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NEWS

# Install 'scider' in R:

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

Bug tracker:https://github.com/chenlaboratory/scider/issues

Datasets:

On BioConductor:scider-1.3.0(bioc 3.20)scider-1.2.0(bioc 3.19)

bioconductor-package

16 exports 1.58 score 133 dependencies

Last updated 2 months agofrom:639189ad8f

Exports:allocateCells corDensity findROI getContour gridDensity mergeROI plotCellCompo plotContour plotCorHeatmap plotDensCor plotDensity plotROI plotSpatial postSelRegion selectRegion spe2PB

Dependencies:abind askpass base64enc Biobase BiocFileCache BiocGenerics bit bit64 blob bslib cachem class classInt cli colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir digest dplyr e1071 evaluate fansi farver fastmap filelock fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue goftest gtable highr hms htmltools htmlwidgets httpuv httr igraph IRanges isoband janitor jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle lubridate lwgeom magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pheatmap pillar pkgconfig plogr plotly polyclip promises proxy purrr R6 rappdirs RColorBrewer Rcpp rjson rlang rmarkdown RSQLite s2 S4Arrays S4Vectors sass scales sf shiny SingleCellExperiment snakecase sourcetools SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.utils stringi stringr SummarizedExperiment sys tensor tibble tidyr tidyselect timechange tinytex UCSC.utils units utf8 vctrs viridisLite withr wk xfun xtable XVector yaml zlibbioc

A quick start guide to the scider package

Ning Liu, Mengbo Li, Yunshun Chen

Rendered fromscider_userGuide.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-10-30
Started: 2023-10-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate all cells with contour level of cell type-specific density.	allocateCells
Check which cells are in which regions	cellsInRegion
Perform kernel density estimation on SpatialExperiment	computeDensity
Draw a contour region on some density level	contour2sf
Test for density correlation between two cell types.	corDensity
Find ROIs based on cell type-specific densities via graph-based method.	findROI
Get contour from density	getContour
Calculate areas between every two density levels	getContourRegions
Combine grids in each ROI to a sf region	grid2sf
Perform kernel density estimation on SpatialExperiment for cell types of interest	gridDensity
Manually merge ROIs	mergeROI
Plot cell type composition in each density level of cell of interest.	plotCellCompo
Plot contour lines.	plotContour
Visualising an sf object (for internal use only at the moment)	plotContourRegion
Plot model statistics using heatmap.	plotCorHeatmap
Plot density correlation between two cell types	plotDensCor
Plot grid-based density.	plotDensity
Plot ROIs on spatial.	plotROI
Plot cells based on spatial coordinates.	plotSpatial
Merge sel_region from the selectRegion function to SpatialExperiment.	postSelRegion
Select region of interest from plot	selectRegion
Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList object	spe2PB