Seurat Files

R toolkit for single cell genomics

This is an exact mirror of the Seurat project, hosted at https://github.com/satijalab/seurat. SourceForge is not affiliated with Seurat.

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Name	Modified	Size	InfoDownloads / Week
Parent folder
README.md	2025-12-13	1.5 kB	0
Version 5.4.0 source code.tar.gz	2025-12-13	3.5 MB	0
Version 5.4.0 source code.zip	2025-12-13	3.8 MB	0
Totals: 3 Items		7.3 MB	0

Changes

Additions

Added support for 10x Space Ranger 4.0 outputs (Visium data with segmentations)
Updated data loading functions Load10X_Spatial, Read10X_Image
Updated GetTissueCoordinates.VisiumV2
Updated spatial visualization functions SpatialPlot, SingleSpatialPlot, SpatialDimPlot, SpatialFeaturePlot
Added helper functions Read10X_Segmentations, Read10X_HD_GeoJson, Format10X_GeoJson_CellID
Added function InteractiveSpatialPlot to allow users to interactively lasso-select cells from a spatial Seurat object (Visium, SlideSeq, or Vizgen data)

Fixes

Updated loading & visualization functions (see above for list) for Visium objects -- see #10125 for details
For binned Visium data, x now correctly corresponds to imagecol from tissue positions; y now correctly corresponds to imagerow from tissue positions; these are now consistent with 10X's coordinate system (with the origin being the top left).
Reverted #10062 in favor of fetching both grouping variables and dimensionality reduction embeddings with FetchData as previously; added warning to alert users when column names of metadata and dimensionality reduction embeddings conflict
Added color retrieval logic in LabelClusters for consistent cluster label coloring (#10198)

Source: README.md, updated 2025-12-13

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