smoppix

Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index

Bioconductor version: 3.23 · Package version: 1.4.0

Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("smoppix")

Details

Maintainer	Stijn Hawinkel <stijn.hawinkel@psb.ugent.be>
Author	Stijn Hawinkel [cre, aut] (ORCID: <https://orcid.org/0000-0002-4501-5180>)
License	GPL-2
URL	https://github.com/sthawinke/smoppix
Bug Reports	https://github.com/sthawinke/smoppix/issues
Downloads rank	287
Source branch	RELEASE_3_23
biocViews	SingleCell, Software, Spatial, Transcriptomics

Documentation

Vignette of the smoppix package

Download

Follow the installation instructions to use this package in your R session.

Source package	smoppix_1.4.0.tar.gz
Windows binary (x86_64)	smoppix_1.4.0.zip
macOS binary (arm64)	smoppix_1.4.0.tgz
macOS binary (x86_64)	smoppix_1.4.0.tgz

Dependencies

Depends: R (>= 4.5.0)

Imports: spatstat.geom (>= 3.2.0), spatstat.random, methods, BiocParallel, SummarizedExperiment, SpatialExperiment, Rdpack, stats, utils, lmerTest, lme4, ggplot2, graphics, grDevices, Rcpp (>= 1.0.11), spatstat.model, openxlsx, Rfast, reformulas, mgcv

LinkingTo: Rcpp

Suggests: testthat, rmarkdown, knitr, DropletUtils, polyCub, RImageJROI, sp, ape, htmltools, funkycells, glmnet, doParallel