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")):
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("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 (>= 4.6) |
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/panoramic/ |
| Package Short Url | https://bioconductor.org/packages/panoramic/ |
| Package Downloads Report | Download Stats |