Coding & Dev Tools

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SWE-bench evaluates AI agents on real-world GitHub bug fixes, testing their ability to generate patches that resolve actual software issues from popular Python repositories.

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Find the most relevant framework/library docs for the requested change.

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Create visual progress updates - charts, before/after comparisons, metrics over time

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Mandatory verification steps for all code reviews to reduce false positives. Load this skill before reporting ANY code review findings.

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Salesforce data operations expert with 130-point scoring. Use when writing SOQL queries, creating test data, performing bulk data operations, or importing/exporting data via sf CLI.

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This skill generates comprehensive chapter content for intelligent textbooks after the book-chapter-generator skill has created the chapter structure. Use this skill when a chapter index.md file exists with title, summary, and concept list, and detailed educational content needs to be generated at the appropriate reading level with rich non-text elements including diagrams, infographics, and MicroSims. (project, gitignored)

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Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.

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Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.

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Coaches users to transform messy data into clean, analysis-ready formats using Power Query UI. Diagnoses data problems, visualizes goals, and guides step-by-step transformations.

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Reviews Phoenix code for controller patterns, context boundaries, routing, and plugs. Use when reviewing Phoenix apps, checking controllers, routers, or context modules.

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Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.

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BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools.

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Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating transcriptomics with FBA.

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Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods. Infer ancient protein sequences and trace evolutionary trajectories through sequence history. Use when inferring ancestral states for protein resurrection or tracing evolutionary history.

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Creates diagrams and animations for STEM education using Matplotlib and Manim. Use for physics diagrams (FBD, vectors), math plots (functions, geometry), flowcharts, or 3Blue1Brown-style animations.

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Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions.

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Datasette - Instant Data Publishing and Exploration

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Set 3-5 strategic goals for the quarter

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Review quarter completion and capture learnings

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Load project context efficiently for Conductor workflows. Use when starting work on a track, implementing features, or needing project context without consuming excessive tokens.

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Workshop an improvement idea into implementation plan

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Interactive wizard for creating Claude Code skills. Use when scaffolding new skills, validating skill structure, managing dependencies, or editing skill configuration files.

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Write failing tests and minimum implementations for TDD team

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Validate a plan before implementation. Use before exiting Plan mode. Pass the plan file path and any additional context files. Returns JSON with findings and score (must reach 9+ to proceed).

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Error Handling Reference

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Error Handling Reference

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Expert equity analyst specializing in stock analysis, valuation, financial...

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Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use when detecting CNVs from WES or targeted panel sequencing data.

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Predict protein-coding genes in eukaryotic genomes using BRAKER3 for combined RNA-seq and protein evidence, or GALBA for protein-only evidence. Runs Augustus with trained parameters for accurate gene models. Use when annotating a newly assembled eukaryotic genome or improving existing gene predictions.

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Detects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Creates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot. Visualizes differential splicing events with grouped samples and junction read support. Use when visualizing specific splicing events or validating differential splicing results.

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Predicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAfold, RNAalifold, RNAcofold). Computes base-pair probabilities, centroid structures, and consensus structures from alignments. Use when predicting RNA folding, evaluating structural stability, or comparing structures across homologs.

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Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio run quality or filtering reads before assembly or alignment.

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Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or converting between annotation formats.

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Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.

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Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).