Discover Data & AI skills, compare source repositories and read the instructions for each workflow.
Audit security with vulnerability scanning, input validation checks, and auth/authz review against OWASP Top 10. Use when implementing authentication, reviewing security-sensitive code, or conducting security a...
This skill should be used when users request help optimizing, improving, or refining their prompts or instructions for AI models. Use this skill when users provide vague, unclear, or poorly structured prompts a...
Translate JSON i18n files to multiple languages with AI-powered quality optimization. Use when user mentions translating JSON, i18n files, internationalization, locale files, or needs to convert language files...
Download YouTube videos, extract English subtitles, translate them to Korean using Claude's own translation capabilities (with video context and web search), and burn Korean subtitles into the video. Use this s...
Generate comprehensive clonality statistics and diversity visualizations for TCR/BCR repertoire analysis. Quantifies clonal expansion, measures diversity metrics (Shannon, Simpson, Gini), and creates publicatio...
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 groups. Genera...
Visualize cell-cell communication inference results from CellCellCommunication process. Creates publication-ready network diagrams, heatmaps, and interaction plots to help interpret ligand-receptor interactions...
Performs enrichment analysis (GSEA-based) for metabolic pathways across different cell groups to identify significantly enriched pathways. Uses fast gene set enrichment analysis (fgsea package) to rank pathways...
Cluster TCR/BCR clones by CDR3 sequences using GIANA or ClusTCR (both Faiss-based). Adds `CDR3_Cluster` column to metadata for clonotype analysis.
Master skill for generating immunopipe pipeline configurations. Determines pipeline architecture based on data type (scRNA-seq with or without scTCR/BCR-seq) and analysis requirements. Routes to individual proc...
Map query single-cell datasets to high-quality reference atlases using Seurat's reference mapping workflow. Performs label transfer, UMAP projection, and integration with reference annotations without modifying...
Configuration skill for immunopipe process
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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), MarkersFinder...
The SampleInfo process is the pipeline entry point that reads sample metadata files, performs statistical analyses, and generates visualization reports.
Calculates pathway activity scores for metabolic pathways across different cell groups and subsets. This process quantifies the metabolic activity of each pathway per group, generating visualizations (heatmaps...
Generates comprehensive cluster statistics and visualizations for Seurat objects, including dimension reduction plots, gene expression visualizations, cluster quality metrics, and clustree diagrams. This proces...
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 by highlig...
Analyzes physicochemical properties of CDR3 amino acid sequences to understand biochemical characteristics of T-cell receptor repertoires. Performs regression analysis between two cell groups at different CDR3...
Pass-through process that prepares Seurat object for metabolic landscape analysis. Routes the processed Seurat object to downstream metabolic analysis processes (MetabolicExprImputation, MetabolicPathwayActivit...
Load pre-existing Seurat objects into the immunopipe pipeline instead of starting from raw count matrices via SampleInfo. This enables analysis on already processed single-cell RNA-seq data stored in Seurat R o...
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) into a S...
Performs fine-grained re-clustering on specific subsets of cells (e.g., individual clusters, cell types, or custom subsets). Unlike `Seurat::FindSubCluster` which only finds subclusters within a single cluster,...
Identifies and visualizes the top expressing genes per cluster in T/B cells, followed by pathway enrichment analysis. Provides quick cluster characterization by highlighting the most highly expressed genes and...
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