smoppix
This is the development version of smoppix; to use it, please install the devel version of Bioconductor.
Analyze Single Molecule Spatial Transcriptomics and Other Spatial Omics Data Using the Probabilistic Index
Bioconductor version: Development (3.21)
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:
Maintainer: Stijn Hawinkel <stijn.hawinkel at psb.ugent.be>
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")| Vignette of the smoppix package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.34 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| 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 |
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.
| Source Package | smoppix_0.99.34.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | smoppix_0.99.34.tgz |
| macOS Binary (arm64) | smoppix_0.99.34.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/smoppix |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/smoppix |
| Bioc Package Browser | https://code.bioconductor.org/browse/smoppix/ |
| Package Short Url | https://bioconductor.org/packages/smoppix/ |
| Package Downloads Report | Download Stats |