pwwang
Publisher on askill
Flexible marker finding process that wraps Seurat's FindMarkers function for custom group comparisons beyond simple cluster-vs-all analysis. Unlike ClusterMarkers (all-vs-all cluster comparisons), Mar...
Generate comprehensive clonality statistics and diversity visualizations for TCR/BCR repertoire analysis. Quantifies clonal expansion, measures diversity metrics (Shannon, Simpson, Gini), and creates...
Performs pseudo-bulk differential gene expression analysis using DESeq2 or edgeR. Aggregates single-cell counts to sample-level pseudo-bulk data, then identifies differentially expressed genes between...
Visualize cell-cell communication inference results from CellCellCommunication process. Creates publication-ready network diagrams, heatmaps, and interaction plots to help interpret ligand-receptor in...
Identifies and visualizes the top expressing genes per cluster across ALL cells (before T/B cell selection), followed by pathway enrichment analysis. Provides initial overview of all cell populations...
Combine scTCR/BCR repertoire data with scRNA-seq expression data using `scRepertoire::combineExpression()`. This process integrates immune receptor information (CDR3 sequences, V(D)J genes, clonotypes...
Infer ligand-receptor interactions and cell-cell communication networks from single-cell RNA-seq data using the LIANA+ framework. Identifies potential signaling events between cell types based on gene...
The SampleInfo process is the pipeline entry point that reads sample metadata files, performs statistical analyses, and generates visualization reports.
Performs fast Gene Set Enrichment Analysis (GSEA) on single-cell data using fgsea R package. Identifies enriched biological pathways by ranking genes based on differential expression between cell grou...
Generates comprehensive cluster statistics and visualizations for Seurat objects, including dimension reduction plots, gene expression visualizations, cluster quality metrics, and clustree diagrams. T...