panoramic
This is the development version of panoramic; to use it, please install the devel version of Bioconductor.
Meta-Analysis of Spatial Colocalization in Spatial Omics
Bioconductor version: Development (3.24)
Provides a pipeline for quantifying and meta-analyzing spatial colocalization between cell types in spatial omics experiments. The package prepares SpatialExperiment inputs, computes Loh-bootstrap spatial summary functions (e.g. L- and K-functions) for cell-type pairs across samples, and performs random-effects meta-analysis to assess group-level differences in spatial colocalization.
Author: Jacob Chang [aut, cre, fnd]
Maintainer: Jacob Chang <jachang4 at stanford.edu>
citation("panoramic")):
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("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 | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6) |
| Imports | dplyr, ggplot2, ggrepel, igraph, tidygraph, ggraph, rlang, S4Vectors, SummarizedExperiment, spatstat.geom, spatstat.explore, BiocParallel, SpatialExperiment, concaveman, metafor, withr, matrixStats, spatstat.utils |
| System Requirements | |
| URL | https://github.com/plevritis-lab/panoramic |
| Bug Reports | https://github.com/plevritis-lab/panoramic/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, 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 | panoramic_0.99.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | panoramic_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/panoramic |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/panoramic |
| Bioc Package Browser | https://code.bioconductor.org/browse/panoramic/ |
| Package Short Url | https://bioconductor.org/packages/panoramic/ |
| Package Downloads Report | Download Stats |