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")):
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")
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/spacexr/ |
| Package Short Url | https://bioconductor.org/packages/spacexr/ |
| Package Downloads Report | Download Stats |