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")):
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("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 | R Script |
| PACE package manual | HTML | R Script |
| 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 (>= 4.6.0) |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PACE_0.99.20.tar.gz |
| Windows Binary (x86_64) | PACE_0.99.20.zip |
| macOS Binary (big-sur-x86_64) | PACE_0.99.20.tgz |
| macOS Binary (sonoma-arm64) | PACE_0.99.20.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PACE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PACE |
| Bioc Package Browser | https://code.bioconductor.org/browse/PACE/ |
| Package Short Url | https://bioconductor.org/packages/PACE/ |
| Package Downloads Report | Download Stats |