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Bioconductor - smoppix (development version)

smoppix

This is the development version of smoppix; for the stable release version, see smoppix.

Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index

Bioconductor version: Development (3.22)

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.

Author: Stijn Hawinkel [cre, aut] ORCID: 0000-0002-4501-5180

Maintainer: Stijn Hawinkel <stijn.hawinkel at psb.ugent.be>

Citation (from within R, enter citation("smoppix")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("smoppix")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("smoppix")
Details biocViews SingleCell, Software, Spatial, Transcriptomics Version 1.1.4 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License GPL-2 Depends R (>= 4.4.0) Imports spatstat.geom (>= 3.2.0), spatstat.random, methods, BiocParallel, SummarizedExperiment, SpatialExperiment, scam, Rdpack, stats, utils, extraDistr, lmerTest, lme4, ggplot2, graphics, grDevices, Rcpp (>= 1.0.11), Matrix, spatstat.model, openxlsx System Requirements URL https://github.com/sthawinke/smoppix Bug Reports https://github.com/sthawinke/smoppix/issues See More Suggests testthat, rmarkdown, knitr, DropletUtils, polyCub, RImageJROI, sp, ape, htmltools, funkycells, glmnet, doParallel Linking To Rcpp Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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