Journal: BMC Bioinformatics

Article Title: SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics

doi: 10.1186/s12859-025-06209-x

Figure Lengend Snippet: SCNT testing on human kidney 10X visium HD dataset. ( A ) Spatial clustering plot based on stPlot showing the distribution of 12 cell clusters across the entire tissue space. ( B ) Spatial distribution of the 12 cell clusters within a sub-region. ( C ) scFeature plot displaying the spatial expression feature of LRP2 within the sub-region

Article Snippet: To demonstrate the functionality of SCNT , we applied it to a 10X Genomics Visium HD dataset of human kidney tissue, following the official tutorial, including dimensionality reduction and clustering.

Techniques: Expressing

Journal: bioRxiv

Article Title: The U-method: Leveraging expression probability for robust biological marker detection

doi: 10.64898/2026.03.31.715470

Figure Lengend Snippet: (A) U-method analysis of scRNA-seq data from lung adenocarcinoma annotated by cell type. UMAP projection of all cell clusters and fibroblast and T-cell subclusters is shown (B) Feature plots showing the top U-markers of the main cell clusters shown in A. (C). Unscaled Dot plots of the top uniquely expressed genes per cluster. (D) Boxplots of U-score distributions across clusters and subclusters. (E) Projection of the average expression of identified markers onto a VisiumHD lung adenocarcinoma sample ( https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt ).

Article Snippet: We then projected the resulting UEG signatures (top 5 UEGs, U-score > 0.2) onto a publicly available lung adenocarcinoma Visium HD section ( https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt ).

Techniques: Expressing, Gene Expression

Journal: bioRxiv

Article Title: The U-method: Leveraging expression probability for robust biological marker detection

doi: 10.64898/2026.03.31.715470

Figure Lengend Snippet: (A) UMAP projections of scRNA-seq data from human colorectal cancer (CRC) and adjacent normal colon tissue split by sample origin, normal or tumor, analyzed by Seurat and annotated by major cell type. (B) Unscaled Dot plot of the top uniquely expressed genes per cluster. (C) Spatial maps showing the projection of uniquely expressed gene (UEG) signatures derived from scRNA-seq of epithelial and cancer cell clusters onto Visium HD CRC tissue sections. For each spot, signature values were computed as the raw average expression of U-method-identified marker genes associated with the epithelial or cancer cluster. No smoothing, normalization, or deconvolution were applied. Spots are plotted at their physical coordinates, with color intensity reflecting the signature value and transparency indicating detectable expression. Scale bar - 300 µm.

Article Snippet: We then projected the resulting UEG signatures (top 5 UEGs, U-score > 0.2) onto a publicly available lung adenocarcinoma Visium HD section ( https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt ).

Techniques: Derivative Assay, Expressing, Marker