Introduction | Installation | Dataset | Tutorial | Load libraries | Load example dataset | SEraster basic functionalities | Rasterize gene expression | Rasterize gene expression within cell-type | Rasterize cell-type | Setting rasterization resolution | Creating and rasterizing permutations | Examples of downstream analyses after SEraster preprocessing | Spatial variable gene (SVG) analysis | Cell-type co-enrichment analysis | Session Information
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
SEraster/json (API)
| # 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
Last updated from:5e2b20c258. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 173 | ||
| linux-devel-x86_64 | OK | 381 | ||
| source / vignettes | OK | 618 | ||
| linux-release-x86_64 | OK | 382 | ||
| macos-release-arm64 | OK | 221 | ||
| macos-oldrel-arm64 | OK | 360 | ||
| windows-devel | OK | 285 | ||
| windows-release | OK | 291 | ||
| windows-oldrel | OK | 325 | ||
| wasm-release | OK | 173 |
Exports:permutateByRotationplotRasterrasterizeCellTyperasterizeGeneExpressionrasterizeMatrix
Dependencies:abindaskpassbackportsBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemcheckmateclassclassIntclicodetoolscpp11curlDBIdbplyrDelayedArraydplyre1071farverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandKernSmoothlabelinglambda.rlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigplyrproxypurrrR6rappdirsRColorBrewerRcpprearrrrjsonrlangRSQLites2S4ArraysS4VectorsS7scalesSeqinfosfSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwkXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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"). | merfish_mousePOA |
| permutateByRotation | permutateByRotation |
| plotRaster | plotRaster |
| rasterizeCellType | rasterizeCellType |
| rasterizeGeneExpression | rasterizeGeneExpression |
| rasterizeMatrix | rasterizeMatrix |
