SpNeigh - Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics
SpNeigh provides methods for neighborhood-aware analysis of spatial transcriptomics data. It supports boundary detection, spatial weighting (centroid- and boundary-based), spatially informed differential expression using spline-based models, and spatial enrichment analysis via the Spatial Enrichment Index (SEI). Designed for compatibility with Seurat objects, SpatialExperiment objects and spatial data frames, SpNeigh enables interpretable, publication-ready analysis of spatial gene expression patterns.
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spatialsinglecellgeneexpressiondifferentialexpressiontranscriptomicssoftware
5.65 score 3 stars 2 scripts 312 downloadsRankMap - Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics
RankMap is a fast and scalable tool for reference-based cell type annotation of single-cell and spatial transcriptomics data. It uses ranked gene expression and multinomial regression to achieve robust predictions, even with partial gene coverage. Compatible with Seurat, SingleCellExperiment, and SpatialExperiment objects, RankMap offers flexible preprocessing and significantly faster runtime than tools like SingleR, Azimuth, and RCTD.
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spatialsinglecelltranscriptomicsgeneexpressionannotationregressionpreprocessingsoftware
5.04 score 2 stars 4 scripts 328 downloads