multipointR
This is the development version of multipointR; to use it, please install the devel version of Bioconductor.
A package to compare intensities of point patterns across samples with spatial parametric models
Bioconductor version: Development (3.24)
`multipointR` is a package to compare the distribution of cells in an image or cross images with point process models. On a single image level point process models (`ppm`) model the spatial distribution of a cell type point pattern as a function of spatial covariates while accounting for natural spacing of cells. The main model class considered in `multipointR` are inhomgoeneous Gibb's point process models. Across multiple images, users can either compare multiple univariate `ppm` models in a for loop or fit one joint model across all images with `mppm`. `multipointR` provides an interface between `SpatialExperiment` and `SpatialFeatureExperiment` objects and let's users flexibly define their own `ppm`/`mppm` models with R's formula interface.
Author: Martin Emons [aut, cre]
, Wolfgang Huber [aut]
, Mark D. Robinson [aut, fnd]
Maintainer: Martin Emons <martin.emons at uzh.ch>
citation("multipointR")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("multipointR")
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("multipointR")| Introduction to `multipointR` | HTML | R Script |
| Reference Manual |
Details
| biocViews | SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.1.0) |
| Imports | SummarizedExperiment, methods, SpatialExperiment, spatstat.geom, spatstat.model, spatstat.explore, formula.tools, mgcv, dplyr, ggplot2, reformulas, S4Vectors, rlang |
| System Requirements | |
| URL | https://github.com/mjemons/multipointR |
| Bug Reports | https://github.com/mjemons/multipointR/issues |
See More
| Suggests | knitr, BiocStyle, patchwork, SpatialFeatureExperiment, rmarkdown, SpatialDatasets, sosta, testthat (>= 3.0.0) |
| Linking To | |
| 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 | multipointR_0.99.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | multipointR_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/multipointR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/multipointR |
| Bioc Package Browser | https://code.bioconductor.org/browse/multipointR/ |
| Package Short Url | https://bioconductor.org/packages/multipointR/ |
| Package Downloads Report | Download Stats |