smoppix
Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index
Bioconductor version: 3.23 · Package version: 1.4.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/smoppix/ |
Citation
From within R, enter citation("smoppix"):
Stijn Hawinkel. smoppix: Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index. doi:10.18129/B9.bioc.smoppix, R package version 1.4.0, https://bioconductor.org/packages/smoppix.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
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