Introduction | Installation | Load packages | Workflow At A Glance | Simulate Example Data | Step 1: Prepare Samples | Step 2: Compute Sample-Level Spatial Effects | Step 3: Pool Across Samples And Test Group Differences | Interpret Pooled And Differential Outputs | One-Call Workflow (panoramic_analyze) | Visualization Tools | Forest Plot (Feature-Level) | Volcano Plot (Global Differential Overview) | Network Summary | Practical Notes | Related Resources
Package: panoramic 0.99.4
Jacob Chang
panoramic: Variance-Aware Multi-Sample Spatial Colocalization Analysis
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.
Authors:
panoramic_0.99.4.tar.gz
panoramic_0.99.4.zip(r-4.7-any)panoramic_0.99.4.zip(r-4.6-any)panoramic_0.99.4.zip(r-4.5-any)
panoramic_0.99.4.tgz(r-4.6-any)panoramic_0.99.4.tgz(r-4.5-any)
panoramic_0.99.4.tar.gz(r-4.7-any)panoramic_0.99.4.tar.gz(r-4.6-any)
panoramic_0.99.4.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)
Last updated from:d45f4c84fb. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 198 | ||
| linux-devel | OK | 308 | ||
| source / vignettes | OK | 273 | ||
| linux-release | OK | 295 | ||
| macos-release | OK | 124 | ||
| macos-oldrel | OK | 123 | ||
| windows-devel | OK | 135 | ||
| windows-release | OK | 152 | ||
| windows-oldrel | OK | 139 | ||
| wasm-release | OK | 192 |
Exports:create_spatial_networkpanoramicpanoramic_analyzepanoramic_extract_contrastpanoramic_meta_mvpanoramic_preparepanoramic_simulate_datasetpanoramic_simulate_spepanoramic_spatialstatsplot_forestplot_representative_samplesplot_spatial_networkplot_volcano
Dependencies:abindaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclassclassIntclicodetoolsconcavemancpp11curlDBIdbplyrDelayedArraydeldirdigestdplyre1071farverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggforceggplot2ggraphggrepelgluegoftestgraphlayoutsgridExtragtablehttr2igraphIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagickmagrittrMASSmathjaxrMatrixMatrixGenericsmatrixStatsmemoisemetadatmetafornlmenumDerivopensslpbapplypillarpkgconfigpolyclipproxypurrrR6RColorBrewerRcppRcppArmadillorjsonrlangRSQLites2S4ArraysS4VectorsS7scalesSeqinfosfSingleCellExperimentsnowSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsyssystemfontstensortibbletidygraphtidyrtidyselecttweenrunitsutf8V8vctrsviridisviridisLitewithrwkXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 |