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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.
Manages PR review polling daemon for automatic notifications and auto-respond.
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…
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…
Comprehensive codebase assessment for agent and production readiness. Scans 8 pillars (48 criteria), verifies commands work, checks GitHub settings. Reports everything, fixes agent readiness only. Tri…
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.
Explore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection. Use for calibration, uncertainty studies, parameter sweeps, LHS sampling, Sob…
Provides comprehensive testing patterns for Spring Boot applications including unit, integration, slice, and container-based testing with JUnit 5, Mockito, Testcontainers, and performance optimization…
Execute a Flow epic or task systematically with git setup, task tracking, quality checks, and commit workflow. Use when implementing a plan or working through a spec. Triggers on /flow-next:work with …
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…
Analyze application logs from the .evlog/logs/ directory. Use when debugging errors, investigating slow requests, understanding request patterns, or answering questions about application behavior. Rea…