Coding & Dev Tools

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File Format Support

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Sync CLAUDE.md from GitHub repository

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Llama Stack Server for development purposes

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Common Ground

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Error Handling Reference

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Error Handling Reference

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Identify and classify repetitive elements and transposable elements using RepeatModeler for de novo repeat library construction and RepeatMasker for genome-wide repeat annotation. Quantify TE expression from RNA-seq with TEtranscripts. Use when masking repeats before gene prediction or analyzing transposable element activity.

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Find cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, or discovering database relationships.

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Permission Set analysis, hierarchy viewer, and "Who has X?" auditing. Use when analyzing permissions, visualizing PS/PSG hierarchies, or finding which Permission Sets grant access to specific objects, fields, or Apex classes.

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Interactive debugging companion for Hive agents - identifies runtime issues and proposes solutions

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Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.

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Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Use when performing TSS proximity analysis, assigning enhancers to genes, defining promoter regions, or finding nearby genomic features.

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Tests genotype-environment associations and identifies loci under local adaptation using LFMM2 (LEA), pcadapt outlier detection, OutFLANK Fst-based selection scans, and redundancy analysis. Detects adaptive genetic variation correlated with environmental variables while controlling for population structure. Use when identifying adaptive loci across environmental gradients, testing for signatures of local adaptation, or predicting genetic vulnerability to climate change with gradientForest.

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Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.

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Controls interactive terminal sessions for running long-lived processes, servers, REPLs, debuggers, and TUI programs without blocking. Use when you need to run dev servers (npm run dev), debuggers (pdb, gdb), REPLs (python, node), databases (psql, mysql), SSH sessions, or editors (vim, nano) — any interactive or blocking program.

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Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by drug-likeness criteria.

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Quick data freshness check. Use when the user asks if data is up to date, when a table was last updated, if data is stale, or needs to verify data currency before using it.

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Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.

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Scaffold repo-local Ralph autonomous harness under scripts/ralph/. Use when user runs /flow-next:ralph-init.

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Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences. Use when predicting MHC binding for vaccine design or neoantigen identification.

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Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predicting structures for novel proteins, protein complexes, or when comparing predictions across multiple methods.

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This skill should be used when the user asks to "improve a skill", "make this skill better", "add features to a skill", "this skill is missing something", "upgrade my skill", "what's missing from this skill", "improve how the skill works step by step", "the skill doesn't do X", "make this more useful", "the skill isn't working well for me", "can this skill do more", or wants to improve skill effectiveness rather than structural correctness.

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Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or inferring variants not directly typed in array data.

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Expert portfolio manager specializing in asset allocation, risk management,...

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Nuanced Classification

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Maps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models. Transfers cell type labels without retraining on combined data. Use when annotating new single-cell datasets using pre-trained reference models.

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Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection. Identifies cell-type-specific splicing patterns. Use when analyzing isoform usage in scRNA-seq or finding splicing differences between cell populations.

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Run local BLAST searches using BLAST+ command-line tools. Use when running fast unlimited searches, building custom databases, performing large-scale analysis, or when NCBI servers are slow or unavailable.

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Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT).

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Data Presentation in Clinical Reports

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Netlify Deployment Patterns

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You are a senior Code Reviewer with 12+ years of experience in software development and code quality assurance. You specialize in identifying code quality issues, performance optimization opportunities, and ensuring adherence to best practices across multiple programming languages and frameworks.

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Used by /flow-next:prime to scan for linting, formatting, type checking, and pre-commit configuration. Do not invoke directly.

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**System Instruction:**

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Search GitHub repos (public + private) for code patterns, implementations, and examples.

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Broader Impacts: Strategies and Best Practices