Package: SEraster 1.5.0

Gohta Aihara

SEraster: Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis

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.

Authors:Gohta Aihara [aut, cre], Mayling Chen [aut], Lyla Atta [aut], Jean Fan [aut, rev]

SEraster_1.5.0.tar.gz
SEraster_1.5.0.zip(r-4.7)SEraster_1.5.0.zip(r-4.6)SEraster_1.5.0.zip(r-4.5)
SEraster_1.5.0.tgz(r-4.6-any)SEraster_1.5.0.tgz(r-4.5-any)
SEraster_1.5.0.tar.gz(r-4.7-any)SEraster_1.5.0.tar.gz(r-4.6-any)
SEraster_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SEraster/json (API)
NEWS

# Install 'SEraster' in R:
install.packages('SEraster', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jefworks-lab/seraster/issues

Datasets:
  • merfish_mousePOA - Preprocessed MERFISH dataset of the mouse preoptic area for a bregma -0.29 slice from a female naive animal (Animal ID = 1, Animal Sex = "Female", Behavior = "Naive", Bregma = "-0.29").

On BioConductor:SEraster-1.5.0(bioc 3.24)SEraster-1.4.0(bioc 3.23)

softwarespatialgeneexpressiontranscriptomicssinglecellpreprocessingspatial-analysisspatial-data-analysisspatial-omicsspatial-transcriptomics

5.84 score 19 stars 18 scripts 246 downloads 5 exports 89 dependencies

Last updated from:5e2b20c258. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE173
linux-devel-x86_64OK381
source / vignettesOK618
linux-release-x86_64OK382
macos-release-arm64OK221
macos-oldrel-arm64OK360
windows-develOK285
windows-releaseOK291
windows-oldrelOK325
wasm-releaseOK173

Exports:permutateByRotationplotRasterrasterizeCellTyperasterizeGeneExpressionrasterizeMatrix

Dependencies:abindaskpassbackportsBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemcheckmateclassclassIntclicodetoolscpp11curlDBIdbplyrDelayedArraydplyre1071farverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandKernSmoothlabelinglambda.rlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigplyrproxypurrrR6rappdirsRColorBrewerRcpprearrrrjsonrlangRSQLites2S4ArraysS4VectorsS7scalesSeqinfosfSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwkXVector

Getting Started With SEraster

Rendered fromgetting-started-with-SEraster.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-01-15
Started: 2023-12-14