Example scripts written in R for
- single-cell data analysis using Seurat package
- analysis of TCR repertoire data using Immunarch package
- survival analysis
- RNA velocity esitmation using Velocyto.R package
- Mutation mapper lollipop plots using cBioPortal and TCGA survival plots
- Shiny App for single-cell data visualization
Single-Cell RNA-seq Explorer (Shiny App)
This interactive Shiny application allows users to visually explore and analyze single-cell RNA-seq data stored in a Seurat object. Key features include:
🧭 Main Functionalities: Dimensionality Reduction Plots (DimPlot): Visualize cells using UMAP, t-SNE, or PCA, colored by various metadata (e.g., clusters, cell types).
Feature Plot: Plot gene expression across cells for selected genes.
Violin Plot: Visualize gene expression distributions across groups (e.g., clusters or cell types), with optional log transformation.
Heatmap: Generate heatmaps for selected gene sets, grouped by metadata, with options to customize display.
QC Tab: Includes:
-Violin plots of quality control metrics (nFeature_RNA, nCount_RNA, percent.mt, percent.ribo)
-Elbow Plot for PCA dimension selection
-Mahalanobis Distance Plot to detect outlier cells based on QC metrics.
Metadata Table: View and search cell-level metadata in a sortable, scrollable table.
⚙️ Customizations & Enhancements:
Dynamically adjust point size, color grouping, and log-transformation. Control gene selection via dropdown or comma-separated input. Improved aesthetics: centered plots, consistent color palettes, larger fonts, and reduced label overlap.