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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
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) | multipointR_0.99.5.tgz |
| 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 |