spacexr
This is the development version of spacexr; to use it, please install the devel version of Bioconductor.
SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics
Bioconductor version: Development (3.21)
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], Gabriel Grajeda [cre]
, Fannie and John Hertz Foundation [fnd]
Maintainer: Gabriel Grajeda <gabriel.grajeda at gmail.com>
citation("spacexr")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 0.99.3 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| 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 | |
| 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_0.99.3.tar.gz |
| Windows Binary (x86_64) | spacexr_0.99.3.zip (64-bit only) |
| macOS Binary (x86_64) | spacexr_0.99.3.tgz |
| macOS Binary (arm64) | spacexr_0.99.3.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 |