spacexr
SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics
Bioconductor version: 3.24 · Package version: 1.5.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Spatial-eXpression-R (spacexr) is a package for analyzing cell types in spatial transcriptomics data. This implementation is a fork of the spacexr GitHub repo (https://github.com/dmcable/spacexr), adapted to work with Bioconductor objects. The original package implements two statistical methods: RCTD for learning cell types and CSIDE for inferring cell type-specific differential expression. Currently, this fork only implements RCTD, which learns cell type profiles from annotated RNA sequencing (RNA-seq) reference data and uses these profiles to identify cell types in spatial transcriptomic pixels while accounting for platform-specific effects. Future releases will include an implementation of CSIDE.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spacexr")Details
| Maintainer | Gabriel Grajeda <gabriel.grajeda@gmail.com> |
| Author | Dylan Cable [aut], Rafael Irizarry [aut] (ORCID: <https://orcid.org/0000-0002-3944-4309>), Gabriel Grajeda [cre] (ORCID: <https://orcid.org/0009-0003-7242-7476>), Fannie and John Hertz Foundation [fnd] |
| License | GPL (>= 3) |
| URL | https://github.com/ggrajeda/spacexr |
| Bug Reports | https://github.com/ggrajeda/spacexr/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, RNASeq, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/spacexr/ |
Citation
From within R, enter citation("spacexr"):
Dylan Cable, Rafael Irizarry. spacexr: SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics. doi:10.18129/B9.bioc.spacexr, R package version 1.5.0, https://bioconductor.org/packages/spacexr.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | spacexr_1.5.0.tar.gz |
| Windows binary (x86_64) | spacexr_1.5.0.zip |
| macOS binary (arm64) | spacexr_1.5.0.tgz |
| macOS binary (x86_64) | spacexr_1.5.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: ggplot2, Matrix, parallel, quadprog, httr, methods, memoise, BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie, SpatialExperiment