Search Skills

Prepares Seurat objects for metabolic landscape analysis, routing to downstream metabolic processes without direct configuration.

Calculates metabolic pathway activity scores across cell groups and visualizes results via heatmaps and violin plots for comparative metabolic state analysis.

Infers ligand-receptor interactions and cell-cell communication networks from single-cell RNA-seq data using the LIANA+ framework.

TESSA integrates TCR sequence and transcriptome data via Bayesian modeling to map functional TCR repertoire landscapes.

Enables targeted differential expression analysis between custom cell groups in single-cell RNA-seq data with automatic pathway enrichment and visualization.

Calculates module scores within the immunopipe bioinformatics pipeline for immune repertoire data analysis.

Analyzes and visualizes top-expressed genes in T/B cell clusters, followed by pathway enrichment for biological characterization.

Generates immunopipe configuration files for single-cell immunology data analysis (scRNA-seq, scTCR/BCR-seq) based on data type and requirements.

Imputes missing values in scRNA-seq data using ALRA, scImpute, or MAGIC to enhance metabolic pathway analysis accuracy.

Processes sample metadata to perform statistical analysis and generate visual reports for data insights.

Core preprocessing for single-cell RNA-seq data using Seurat, including QC, normalization, and multi-sample integration for downstream analysis.

Loads pre-processed single-cell RNA-seq data from Seurat R objects into immunopipe for analysis, bypassing raw data processing steps.

Guides optimal structure and content for project documentation including READMEs, docs directories, and technical files.

Guides strategic code refactoring decisions for legacy systems and technical debt reduction.

Evaluates test completeness using a 7-dimensional framework to ensure high-quality test coverage during development and review.

Guides developers through pre-commit quality gates and code check-in workflow validation.

Provides semantic versioning and changelog formatting standards for software releases.

Generates and maintains CHANGELOG.md files adhering to Keep a Changelog conventions for versioned release documentation.

Generates Software Design Documents (SDD) from legacy codebases by analyzing structure and functionality for comprehensive system documentation.

Standardizes API error code design using PREFIX_CATEGORY_NUMBER format for consistent error handling and API development.

Guides developers through pre-commit quality gates and workflow validation before code submission.

Guides the creation of software requirements, user stories, and feature specifications for effective project planning and execution.

Guides development teams through Acceptance Test-Driven Development (ATDD) to define acceptance criteria, write user stories, and secure product owner sign-off.

Assesses test coverage completeness using a 7-dimensional framework to ensure high-quality test suites.