panoramic
This is the development version of panoramic; to use it, please install the devel version of Bioconductor.
Variance-Aware Multi-Sample Spatial Colocalization Analysis
Bioconductor version: Development (3.24)
Quantifies and compares cell-type spatial colocalization across samples, patients, and conditions in spatial omics studies. Its primary statistic, edge-corrected local competition enrichment, measures excess or deficit local mixing for ordered cell-type pairs on a percentage-point scale. The package estimates within-sample uncertainty with spatial bootstrap procedures and propagates it through multilevel random-effects meta-analysis for pooled inference and group-level contrasts; classical spatial summary statistics are also supported.
Author: Jacob Chang [aut, cre, fnd] 
Maintainer: Jacob Chang <jachang4 at stanford.edu>
citation("panoramic")):Jacob Chang. panoramic: Variance-Aware Multi-Sample Spatial Colocalization Analysis. doi:10.18129/B9.bioc.panoramic, R package version 0.99.4, https://bioconductor.org/packages/panoramic.
Generated from the package metadata; it may differ from the package's own citation.
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("panoramic")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("panoramic")| PANORAMIC tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | SingleCell, Software, Spatial |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5) |
| Imports | dplyr, ggplot2, ggrepel, igraph, tidygraph, ggraph, rlang, S4Vectors, SummarizedExperiment, spatstat.geom, spatstat.explore, BiocParallel, SpatialExperiment, concaveman, metafor, withr, matrixStats |
| System Requirements | |
| URL | https://github.com/plevritis-lab/panoramic |
| Bug Reports | https://github.com/plevritis-lab/panoramic/issues |
See More
| Suggests | knitr, markdown, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | panoramic_0.99.4.tar.gz |
| Windows Binary (x86_64) | panoramic_0.99.4.zip |
| macOS Binary (big-sur-x86_64) | panoramic_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | panoramic_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/panoramic |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/panoramic |
| Package Short Url | https://bioconductor.org/packages/panoramic/ |
| Package Downloads Report | Download Stats |