Development Claude Skills
8 676 development skills from 759 authors. They write and change code. Half of them fit into 1 830 tokens or less — that is what one costs your context window when the agent loads it. 1 213 ship runnable scripts rather than instructions alone. 42 of them cannot work without an MCP server, most often rube. We also found 1 172 copies of these same skills sitting in other people's repositories — counted once here, not 1 172 times.
8 676 unique 759 authors 5 250 updated this month 1 369 from vendors
Check release readiness and trigger the release pipeline for Azure SDK packages. **UTILITY SKILL**. USE FOR: "release SDK", "trigger release", "check release readiness", "release pipeline", "publish package", "ship SDK". DO NOT USE FOR: SDK development, code generation, pipeline debugging, release plan creation. INVOKES: azure-sdk-mcp:azsdk_release_sdk.
**WORKFLOW SKILL** — Iteratively improve skill frontmatter compliance using the Ralph loop pattern. WHEN: \"run sensei\", \"sensei help\", \"improve skill\", \"fix frontmatter\", \"skill compliance\", \"frontmatter audit\", \"score skill\", \"check skill tokens\". INVOKES: token counting tools, test runners, git commands. FOR SINGLE OPERATIONS: use token CLI directly for counts/checks.
Create, get, update, abandon, and link SDK PRs to release plan work items for Azure SDK releases. **UTILITY SKILL**. USE FOR: "create release plan", "get release plan", "update release plan", "update API spec in release plan", "update SDK details in release plan", "abandon release plan", "link SDK PR to plan", "namespace approval", "check release plan status". DO NOT USE FOR: SDK code generation, pipeline troubleshooting, API review feedback. INVOKES: azure-sdk-mcp:azsdk_create_release_plan, azure-sdk-mcp:azsdk_get_release_plan, azure-sdk-mcp:azsdk_get_release_plan_for_spec_pr, azure-sdk-mcp:azsdk_update_release_plan, azure-sdk-mcp:azsdk_update_api_spec_pull_request_in_release_plan, azure-sdk-mcp:azsdk_update_sdk_details_in_release_plan, azure-sdk-mcp:azsdk_abandon_release_plan, azure-sdk-mcp:azsdk_link_sdk_pull_request_to_release_plan, azure-sdk-mcp:azsdk_link_namespace_approval_issue.
Creates or adds Convex to an app. Use for new Convex projects, npm create convex@latest, frontend setup, env vars, or the first npx convex dev run.
Audits Convex performance for reads, subscriptions, write contention, and function limits. Use for slow features, insights findings, OCC conflicts, or read amplification.
Sets up Convex auth, identity mapping, and access control. Use for login, auth providers, users tables, protected functions, or roles in a Convex app.
Self-contained app generator — invoke this skill directly, do not decompose into sub-steps. Generates React web apps with TinyBase reactive data store. Use when creating new web applications, adding components, or working with real-time data. Ideal for quick prototypes and single-page apps that need real-time data sync.
Self-contained app generator — invoke this skill directly, do not decompose into sub-steps. Generates React web apps with TinyBase reactive data store. Use when creating new web applications, adding components, or working with real-time data. Ideal for quick prototypes and single-page apps that need real-time data sync.
Framework for competitive landscape analysis across any industry. Use when creating competitor analysis, market positioning assessments, investment memos, strategic reviews, or any analysis requiring systematic evaluation of competitive dynamics. Triggers include requests for competitive landscape decks, peer comparisons, market structure analysis, strategic positioning assessments, and investment recommendations.
Guide for quality focused software architecture. This skill should be used when users want to write code, design architecture, analyze code, in any case that relates to software development.
Build product roadmaps with quarterly planning, feature prioritization, dependency mapping, and stakeholder alignment. Create actionable roadmaps that communicate strategy and guide execution.
PM skill for Claude Code, Codex, Cursor, and Windsurf. Diagnoses SaaS metrics, critiques PRDs, plans roadmaps, runs discovery, coaches PM career transitions, pressure-tests AI product decisions, and designs PLG growth strategies. Seven knowledge domains, 12 templates, 40+ frameworks, and an opinionated interaction style that labels assumptions and names tradeoffs.
> Compress natural language memory files (CLAUDE.md, todos, preferences) into caveman format to save input tokens. Preserves all technical substance, code, URLs, and structure. Compressed version overwrites the original file. Human-readable backup saved as FILE.original.md.
Apply Google Style documentation standards to Python, Go, and Terraform code. Use when writing or reviewing code that needs docstrings/comments, when asked to "document this code", "add docstrings", "follow Google Style", or when improving code documentation quality. Supports Python docstrings, Go comments, and Terraform variable/output descriptions. Enforces consistent, professional documentation standards.
Generate comprehensive, professional project documentation structures including README, ARCHITECTURE, USER_GUIDE, DEVELOPER_GUIDE, and CONTRIBUTING files. Use when the user requests project documentation creation, asks to "document a project", needs standard documentation files, or wants to set up docs for a new repository. Adapts to Python/Go projects and OpenSource/internal contexts.
This skill should be used when the user asks to validate, reindex, repair registries, check links, check continuity, count words, summarize a story project, import an existing manuscript, export a manuscript, run the story CLI, or perform deterministic maintenance on a Story Skills markdown project.
Comprehensive GitHub repository management toolkit. Provides file editing, issue/PR management, GitFlow workflow, release management, commit investigation, CI/CD workflow creation, and configuration file generation via MCP GitHub tools.
> Structure prediction using Chai-1, a foundation model for molecular structure. (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For ESM-based analysis, use esm.
> Generate protein backbones using RFdiffusion, a diffusion-based generative (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers. For sequence design after backbone generation, use proteinmpnn. For structure validation, use alphafold or chai. For QC thresholds, use protein-qc.
Python-first workflow for bulk RNA-seq expression intake, normalization, sample QC, and downstream-ready matrices.
> Chai-1 structure prediction for protein complexes and design validation. (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-design-qc. For AlphaFold2 prediction, use alphafold2-multimer. For ESM-based analysis, use esm2-sequence-scoring.
Workflow for de novo assembly, scaffolding, polishing, contamination review, and assembly QC.
Workflow for pseudotime, lineage branching, and state-transition analysis in single-cell data.
ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.
Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.
Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.
Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).
Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and DEqMS workflows with empirical Bayes moderation, fold change shrinkage for accurate effect size estimation, and Python alternatives. Use when identifying proteins with significant abundance changes between experimental groups.
Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.
Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.
Build circular genome visualizations using circlize (R), pyCirclize (Python), or Circos (Perl CLI) with ideogram tracks, multi-data tracks (scatter, histogram, heatmap), chord/link arcs for interactions, and explicit circos.clear() between plots. Covers when circular is appropriate vs when Cartesian wins (Cleveland-McGill 1984), karyograms, and chromosome adjacency in chord diagrams. Use when adjacency on the circle conveys meaning — chromosome-level overview, structural variants, Hi-C interactions, cross-genome comparisons.
Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.
Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.
Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clustering with Leiden/Louvain algorithms, generating UMAP/tSNE embeddings, and visualizing clusters. Use when performing dimensionality reduction and clustering on single-cell data.
Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.
End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, choosing the correct hit-calling method by experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats. Use when loading, saving, or converting single-cell data formats.
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.
Use when a workflow has explicit data dependencies, independently executable branches, typed joins, or node-local recovery needs that justify a bounded static dependency graph.
Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.
Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens. Covers on-target scoring (Rule Set 2, Azimuth, DeepSpCas9, CRISPRon), off-target scoring (CFD, MIT), TSS-relative positioning for CRISPRi/a (Horlbeck, Dolcetto, Calabrese), PAM-variant chemistries, control-guide composition, oligo cloning architecture, and library QC. Use when choosing a genome-wide library (GeCKOv2 vs Avana vs Brunello vs TKOv3 vs Inzolia), designing a focused or paralog-focused custom library, picking CRISPRi vs CRISPRa TSS windows, deciding control-guide proportions, or diagnosing library skew and dropout in a freshly cloned pool.
Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for differential expression between clusters, identifying cluster-specific markers, scoring gene sets, and assigning cell type labels. Use when finding marker genes and annotating clusters.
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic profiling output.
Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessing.
Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.
Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.