SEraster
This is the development version of SEraster; for the stable release version, see SEraster.
Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis
Bioconductor version: Development (3.24)
SEraster is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. SEraster reduces the number of spatial points in spatial omics datasets for downstream analysis through a process of rasterization where single cells’ gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. SEraster is built on an R/Bioconductor S4 class called SpatialExperiment. SEraster can be incorporated with other packages to conduct downstream analyses for spatial omics datasets, such as detecting spatially variable genes.
Author: Gohta Aihara [aut, cre]
, Mayling Chen [aut]
, Lyla Atta [aut]
, Jean Fan [aut, rev]
Maintainer: Gohta Aihara <gohta.aihara at gmail.com>
citation("SEraster")):
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("SEraster")
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("SEraster")| Getting Started With SEraster | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | BiocParallel, ggplot2, Matrix, methods, rearrr, sf, SpatialExperiment, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/JEFworks-Lab/SEraster |
| Bug Reports | https://github.com/JEFworks-Lab/SEraster/issues |
See More
| Suggests | CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr, rmarkdown, BiocManager, remotes |
| 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 | SEraster_1.5.0.tar.gz |
| Windows Binary (x86_64) | SEraster_1.5.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SEraster_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | SEraster_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SEraster |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SEraster |
| Bioc Package Browser | https://code.bioconductor.org/browse/SEraster/ |
| Package Short Url | https://bioconductor.org/packages/SEraster/ |
| Package Downloads Report | Download Stats |