PACE
This is the development version of PACE; to use it, please install the devel version of Bioconductor.
Proximity-Associated Changes in Expression for Spatial Transcriptomics
Bioconductor version: Development (3.24)
PACE (Proximity-Associated Changes in Expression) is a hierarchical empirical Bayes framework that quantifies how a cell's gene expression changes with proximity to specific neighbouring cell types in imaging-based spatial transcriptomics such as Xenium and CosMx. It fits negative binomial mixed models with partial pooling across cell types, corrects for transcript contamination between adjacent cells with a per-cell ambient term, and decomposes expression variance into cell-type identity, spatial cell state, contamination, and residual components. Input and output follow SpatialExperiment conventions.
Author: Elijah Willie [aut, cre] 
, Shreya Rajesh Rao [aut], John Ormerod [aut], Ellis Patrick [aut], Australian Government Research Training Program [fnd]
Maintainer: Elijah Willie <ewil3501 at uni.sydney.edu.au>
citation("PACE")):Elijah Willie, Shreya Rajesh Rao, John Ormerod, Ellis Patrick. PACE: Proximity-Associated Changes in Expression for Spatial Transcriptomics. doi:10.18129/B9.bioc.PACE, R package version 0.99.20, https://bioconductor.org/packages/PACE.
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("PACE")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("PACE")| Comparing proximity effects between conditions | HTML |
| PACE package manual | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, GeneExpression, Regression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.20 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | methods, stats, utils, Rcpp, Matrix, SpatialExperiment, S4Vectors, SummarizedExperiment, BiocParallel, dplyr, tidyr, tibble, spatstat.geom, MASS, dbscan, lme4, mashr, ashr, ggplot2, patchwork, scales, stringr |
| System Requirements | GNU GSL |
| URL | https://github.com/ecool50/PACE https://ecool50.github.io/PACE |
| Bug Reports | https://github.com/ecool50/PACE/issues |
See More
| Suggests | DelayedArray, glmmTMB, broom.mixed, glue, testthat (>= 3.0.0), R6, knitr, rmarkdown, BiocStyle |
| Linking To | Rcpp, RcppEigen |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/PACE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PACE |
| Package Short Url | https://bioconductor.org/packages/PACE/ |
| Package Downloads Report | Download Stats |