spacexr
This is the released version of spacexr; for the devel version, see spacexr.
SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics
Bioconductor version: Release (3.23)
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.
Author: Dylan Cable [aut], Rafael Irizarry [aut] 
, Gabriel Grajeda [cre] , Fannie and John Hertz Foundation [fnd]
Maintainer: Gabriel Grajeda <gabriel.grajeda at gmail.com>
citation("spacexr")):Dylan Cable, Rafael Irizarry. spacexr: SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics. doi:10.18129/B9.bioc.spacexr, R package version 1.4.0, https://bioconductor.org/packages/spacexr.
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")
BiocManager::install("spacexr")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("spacexr")| rctd-tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5.0) |
| Imports | ggplot2, Matrix, parallel, quadprog, httr, methods, memoise, BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie, SpatialExperiment |
| System Requirements | |
| URL | https://github.com/ggrajeda/spacexr |
| Bug Reports | https://github.com/ggrajeda/spacexr/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| 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 | spacexr_1.4.0.tar.gz |
| Windows Binary (x86_64) | spacexr_1.4.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | spacexr_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | spacexr_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spacexr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spacexr |
| Package Short Url | https://bioconductor.org/packages/spacexr/ |
| Package Downloads Report | Download Stats |