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Jujutsu (`jj`) is a Git-compatible version control system with a simpler mental model - no staging area, working copy is always a commit, and conflicts don't block operations. Use this skill for versi…
Provides testing strategies for LangChain4j-powered applications. Handles mocking LLM responses, testing retrieval chains, and validating AI workflows. Use when testing AI-powered features reliably.
This skill should be used when implementing fault tolerance and resilience patterns in Spring Boot applications using the Resilience4j library. Apply this skill to add circuit breaker, retry, rate lim…
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysi…
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and…
Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC. Use when evaluating data suitability …
Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or h…
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Use when creating a git worktree for feature isolation with automatic environment setup including .env files and dependency installation
Automatically updates project documentation by analyzing git changes between the current branch and the last release tag. Performs git diff analysis to identify modifications, then updates README.md, …
Provides comprehensive testing patterns for Spring Boot applications including unit, integration, slice, and container-based testing with JUnit 5, Mockito, Testcontainers, and performance optimization…
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages i…
Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifying cell populations through hierarchical gating strat…
Test CLI applications interactively using tmux sessions. Use when testing TUI apps (ratatui dashboard, interactive prompts), verifying CLI command output, testing keyboard navigation, or validating te…
Use when an agent is asked to define, review, or write acceptance criteria for a request or plan. Derives acceptance criteria from the current request context, confirms them with the user, and writes …
Provides patterns for enabling and operating the Spring Cache abstraction in Spring Boot. Use when implementing application-level caching for performance-sensitive workloads.
Provides patterns for unit testing caching behavior using Spring Cache annotations (@Cacheable, @CachePut, @CacheEvict). Use when validating cache configuration and cache hit/miss scenarios.
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant call…
Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative …
Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes using WGCNA and CEMiTool. Detects hub genes and module-trait relationships from bulk …
Plan and evaluate mesh generation for numerical simulations. Use when choosing grid resolution, checking aspect ratios/skewness, estimating mesh quality constraints, or planning adaptive mesh refineme…