Yano is an R package for spatial dissimilarity analysis（空间不相似算法）in single-cell transcriptomics. It detects features (such as genes, exons, junctions, or genetic variants) whose spatial expression patterns differ from a reference (e.g., the host gene or an alternative assay). The method works on any spatial embedding: PCA, UMAP, spatial coordinates, lineage trajectories, or integration spaces like Harmony.
Alternative splicing detection compares exon and junction expression against their host genes to identify differential isoform usage across cell populations.
Allele-specific expression tests whether maternal and paternal alleles show divergent spatial patterns.
Other functions include genetic variant annotation for scRNA-seq, interactive cell selection, and track visualization.
Yano's core is the spatial dissimilarity test. For each feature, it computes a spatial dissimilarity statistic between the feature and its binding feature, and compares it against a null distribution generated by permutation. Features whose spatial pattern deviates significantly from the binding feature are reported. The method does not depend on clustering or differential expression. It operates directly on the cell-by-cell spatial neighborhood graph, making it sensitive to subtle, spatially coherent signals even for lowly expressed features.
if (!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("shiquan/Yano")
- Alternative splicing analysis for scRNA-seq
- Allele-specific gene expression analysis for scRNA-seq
- Annotating and prioritizing genetic variants for scRNA-seq
- Perform alternative splicing analysis for multiple Visium samples
- Select cells from reduction maps and spatial locations
- Perform alternative splicing analysis for cell trajectory and user-defined embeddings
Shi, Q., & Kristiansen, K. (2025). Spatial dissimilarity analysis in single cell transcriptomics. Cell Reports Methods. https://doi.org/10.1016/j.crmeth.2025.101141