SEraster
Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis
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)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SEraster")Details
| Maintainer | Gohta Aihara <gohta.aihara@gmail.com> |
| Author | Gohta Aihara [aut, cre] (ORCID: <https://orcid.org/0000-0002-2492-9610>), Mayling Chen [aut] (ORCID: <https://orcid.org/0009-0009-0961-6665>), Lyla Atta [aut] (ORCID: <https://orcid.org/0000-0002-6113-0082>), Jean Fan [aut, rev] (ORCID: <https://orcid.org/0000-0002-0212-5451>) |
| License | GPL-3 |
| URL | https://github.com/JEFworks-Lab/SEraster |
| Bug Reports | https://github.com/JEFworks-Lab/SEraster/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/SEraster/ |
Citation
From within R, enter citation("SEraster"):
Gohta Aihara, Mayling Chen, Lyla Atta, Jean Fan. SEraster: Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis. doi:10.18129/B9.bioc.SEraster, R package version 1.5.0, https://bioconductor.org/packages/SEraster.
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 | SEraster_1.5.0.tar.gz |
| Windows binary (x86_64) | SEraster_1.5.0.zip |
| macOS binary (arm64) | SEraster_1.5.0.tgz |
| macOS binary (x86_64) | SEraster_1.5.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocParallel, ggplot2, Matrix, methods, rearrr, sf, SpatialExperiment, SummarizedExperiment
Suggests: CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr, rmarkdown, BiocManager, remotes