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Docs, README files, API references, tutorials, specs, and changelogs
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Showing 10,441–10,464 of 15,624 skills
- Gene Tree Species Tree ReconciliationReconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signa...Votes: 0GitHub stars: 1,198
- Comparative Annotation ProjectionProject gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma, Schwede & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2021 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying g...Votes: 0GitHub stars: 1,198
- Clip QcComprehensive 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 ...Votes: 0GitHub stars: 1,198
- Cut And Run TagAnalyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli sp...Votes: 0GitHub stars: 1,198
- Molecular StandardizationStandardizes molecular structures using the ChEMBL structure pipeline for normalization and parent selection plus RDKit rdMolStandardize for explicit custom steps such as tautomer canonicalization, salt/solvent stripping, charge handling, stereochemistry handling, mixture selection, and isotope normalization. Explicitly compares ChEMBL, canSARchem, RDKit, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compoun...Votes: 0GitHub stars: 1,198
- Genomic SemFits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modelin...Votes: 0GitHub stars: 1,198
- Genetic CorrelationEstimates bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitiv...Votes: 0GitHub stars: 1,198
- Documentation TemplatesDocumentation templates and structure guidelines. README, API docs, code comments, and AI-friendly documentation.Votes: 0GitHub stars: 227
- Documentation Generation Doc GenerateYou are a documentation expert specializing in creating comprehensive, maintainable documentation from code. Generate API docs, architecture diagrams, user guides, and technical references using AI...Votes: 0GitHub stars: 227
- Docs ArchitectCreates comprehensive technical documentation from existingVotes: 0GitHub stars: 227
- Doc CoauthoringGuide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical specs, decision docs, or similar structured content. This ...Votes: 0GitHub stars: 227
- Conductor New TrackCreate a new track with specification and phased implementation planVotes: 0GitHub stars: 227
- CommitCreate commit messages following Sentry conventions. Use when committing code changes, writing commit messages, or formatting git history. Follows conventional commits with Sentry-specific issue re...Votes: 0GitHub stars: 227
- Code Documentation Doc GenerateYou are a documentation expert specializing in creating comprehensive, maintainable documentation from code. Generate API docs, architecture diagrams, user guides, and technical references using AI...Votes: 0GitHub stars: 227
- BrainstormingUse before creative or constructive work (features, architecture, behavior). Transforms vague ideas into validated designs through disciplined reasoning and collaboration.Votes: 0GitHub stars: 227
- Binary Analysis PatternsMaster binary analysis patterns including disassembly, decompilation, control flow analysis, and code pattern recognition. Use when analyzing executables, understanding compiled code, or performing...Votes: 0GitHub stars: 227
- Azure Compute Batch Java|Votes: 0GitHub stars: 227
- Api DocumenterMaster API documentation with OpenAPI 3.1, AI-powered tools, andVotes: 0GitHub stars: 227
- Algorithmic ArtCreating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields,...Votes: 0GitHub stars: 227
- Multimodal Corpus IngestionNormalize mixed inputs like code, docs, PDFs, screenshots, diagrams, audio, and transcripts into a structured corpus. Use when the task depends on combining multiple artifact types before analysis or retrieval.Votes: 0GitHub stars: 8
- Pr Review CanvasGenerate an interactive PR review walkthrough as an HTML page. Fetches PR data via gh API, categorizes files into core vs mechanical changes, adds reviewer annotations, and renders diffs with moved-code detection. Use when the user pastes a GitHub PR URL and asks for a review, walkthrough, or summary, or says \\\"review this PR\\\".Votes: 0GitHub stars: 8
- Plugin DevThis skill should be used when creating extensions for Claude Code or OpenCode, including plugins, commands, agents, skills, and custom tools. Covers both platforms with format specifications, best practices, and the ai-eng-system build system.Votes: 0GitHub stars: 8
- Knowledge ArchitectureBuild a static-first knowledge architecture using file-backed domain maps, rules, hypotheses, and durable references. Use for knowledge architecture, learning systems, decision context, and long-lived team memory without runtime memory tooling.Votes: 0GitHub stars: 8
- Source Driven DevelopmentGround every framework decision in official documentation. Use when you want authoritative, source-cited code for any framework or library.Votes: 0GitHub stars: 8