Package: panoramic 0.99.3

Jacob Chang

panoramic: Meta-Analysis of Spatial Colocalization in Spatial Omics

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.

Authors:Jacob Chang [aut, cre, fnd]

panoramic_0.99.3.tar.gz
panoramic_0.99.3.zip(r-4.7)panoramic_0.99.3.zip(r-4.6)panoramic_0.99.3.zip(r-4.5)
panoramic_0.99.3.tgz(r-4.6-any)panoramic_0.99.3.tgz(r-4.5-any)
panoramic_0.99.3.tar.gz(r-4.7-any)panoramic_0.99.3.tar.gz(r-4.6-any)
panoramic_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
panoramic/json (API)

# Install 'panoramic' in R:

install.packages('panoramic', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/plevritis-lab/panoramic/issues

On BioConductor:panoramic-0.99.3(bioc 3.24)

software spatial singlecell

4.85 score 2 stars 3 scripts 76 downloads 13 exports 117 dependencies

Last updated from:ca3f3cacb6. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	239
linux-devel-x86_64	OK	284
source / vignettes	OK	286
linux-release-x86_64	OK	271
macos-release-arm64	OK	110
macos-oldrel-arm64	OK	125
windows-devel	OK	152
windows-release	OK	129
windows-oldrel	OK	133
wasm-release	OK	187

Exports:create_spatial_network panoramic panoramic_analyze panoramic_extract_contrast panoramic_meta_mv panoramic_prepare panoramic_simulate_dataset panoramic_simulate_spe panoramic_spatialstats plot_forest plot_representative_samples plot_spatial_network plot_volcano

Dependencies:abind askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob cachem class classInt cli codetools concaveman cpp11 curl DBI dbplyr DelayedArray deldir digest dplyr e1071 farver fastmap filelock formatR futile.logger futile.options generics GenomicRanges ggforce ggplot2 ggraph ggrepel glue goftest graphlayouts gridExtra gtable httr2 igraph IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle magick magrittr MASS mathjaxr Matrix MatrixGenerics matrixStats memoise metadat metafor nlme numDeriv openssl pbapply pillar pkgconfig polyclip proxy purrr R6 RColorBrewer Rcpp RcppArmadillo rjson rlang RSQLite s2 S4Arrays S4Vectors S7 scales Seqinfo sf SingleCellExperiment snow SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment sys systemfonts tensor tibble tidygraph tidyr tidyselect tweenr units utf8 V8 vctrs viridis viridisLite withr wk XVector

PANORAMIC tutorial

Rendered fromtutorial.Rmdusingknitr::rmarkdown

Last update: 2026-04-21
Started: 2025-12-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Internal: custom Loh bootstrap with overlap-weighted blocks	.lohboot_block_weighted
Internal: local function info (spatstat helper)	.spatstat_local_function_info
Construct spatial colocalization network from PANORAMIC results	create_spatial_network
Run PANORAMIC End-To-End	panoramic
Run PANORAMIC end-to-end, including pooling/meta-analysis	panoramic_analyze
Extract PANORAMIC Contrast, Meta, or Spatialstats Tables	panoramic_extract_contrast
Multilevel Random-Effects Meta-Analysis of PANORAMIC Features	panoramic_meta_mv
Prepare PANORAMIC inputs from a list of SpatialExperiment objects	panoramic_prepare
Simulate a two-group PANORAMIC example dataset	panoramic_simulate_dataset
Simulate one SpatialExperiment object for PANORAMIC examples	panoramic_simulate_spe
Compute Pairwise Spatial Statistics for PANORAMIC	panoramic_spatialstats
Forest Plot for PANORAMIC Spatial Colocalization	plot_forest
Plot Representative Samples for Significant Differential Hits	plot_representative_samples
Plot PANORAMIC spatial colocalization network	plot_spatial_network
Volcano plot for differential spatial colocalization	plot_volcano