4K skills · sorted by relevance
Connect Codex to any app via the Composio CLI. Send emails, create issues, post messages, update databases - take real actions across Gmail, Slack, GitHub, Notion, and 1000+ services from the terminal.
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Help address review/issue comments on the open GitHub PR for the current branch using gh CLI; verify gh auth first and prompt the user to authenticate if not logged in.
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Automate Bitbucket repositories, pull requests, branches, issues, and workspace management via Rube MCP (Composio). Always search tools first for current schemas.
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Use when you need to address review or issue comments on an open GitHub Pull Request using the gh CLI.
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Use when a coding task should be driven end-to-end from issue intake through implementation, review, deployment, and acceptance verification with minimal human re-intervention.
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Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.
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Segment single cells from multiplexed IMC/MIBI tissue images using Mesmer/DeepCell, Cellpose, or ilastik+CellProfiler, covering whole-cell vs nuclear segmentation, the summed-membrane-channel decision, nuclear-expansion bias, lateral spillover, resolution-floor parameters, and downstream-proxy evaluation. Use when delineating cells after preprocessing, choosing a segmentation model, building a cell mask for quantification, diagnosing impossible double-positive populations, or troubleshooting over/under-segmentation.
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Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and integration with HLA-LOH and neoantigen quality (Luksza 2017 fitness). Use when assessing ICI eligibility under tumor-specific cutoffs (McGrail 2021), comparing tissue vs bTMB, or auditing TMB-H reporting against ESMO 2024 and FDA pembrolizumab pan-tumor 2020.
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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.
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Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.
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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.
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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.
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Run build, deploy, inspect, and fix loops for .NET MAUI apps that already have MAUI DevFlow integrated. USE FOR: launching MAUI apps, selecting devices or emulators, waiting for or recovering agent connections, broker/port/adb connectivity issues, visual tree inspection, screenshots, UI interaction, Blazor WebView CDP debugging, reading DevFlow logs, and iterative app debugging. DO NOT USE FOR: first-time DevFlow package setup (use maui-devflow-onboard), or generic desktop automation unrelated to MAUI. INVOKES: maui devflow CLI, dotnet CLI, Android adb/android tools, and Apple simctl tools.
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Use this skill when buying a used tractor or trailer. Covers verifying compliance status, hidden issues, and what to inspect before signing.
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Use this skill for wheel-end maintenance and lubrication. Covers oil-bath vs grease packs, wheel-end loss issues, and inspection intervals.
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Use this skill when a driver holds CDLs in multiple states or has resided in multiple states. Covers what MVRs to pull, federal recordkeeping requirements, and state-specific issues.
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Use this skill to verify that a driver's medical certificate was issued by a certified examiner on the FMCSA National Registry. Covers the search process, what to verify, and how to handle examiner removal.
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Use this skill when the user asks about CDL driver wellness, retention strategies, what causes driver turnover, common health issues (obesity, hypertension, sleep apnea, mental health), benefits packages, home-time policies, and how to build a culture that keeps drivers. Reference ATA Workforce Development + FMCSA Wellness Initiative.
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Use when optimizing Docker builds with BuildKit, designing multi-stage Dockerfiles, leveraging cache mounts, building multi-arch images, choosing distroless vs alpine, or signing images with cosign. Triggers: docker build slow, layer cache not hitting, npm install / pip install reruns, multi-stage final image bloat, glibc vs musl issues, RUN --mount=type=cache, BUILDKIT_INLINE_CACHE, registry cache exporters, qemu emulation for arm64, COPY ordering for cache. NOT for Docker daemon admin, Kubernetes-specific image policies, container security scanning workflows, or Buildpacks (different paradigm).
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Analyze existing XML sitemaps or generate new ones with industry templates. Validates format, URLs, and structure. Use when user says "sitemap", "generate sitemap", "sitemap issues", or "XML sitemap".
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Technical SEO audit across 9 categories: crawlability, indexability, security, URL structure, mobile, Core Web Vitals, structured data, JavaScript rendering, and IndexNow protocol. Use when user says "technical SEO", "crawl issues", "robots.txt", "Core Web Vitals", "site speed", or "security headers".
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The re-measure and standing report of the canonical data model's live DB conformance. Use when asked 'where are we at' on DB drift or conformance, to update the drift numbers, when a drift-audit brief is re-issued, or on /drift-audit. NOT the per-table fix recipe (use matrx-frontend's db-canonicalize-table).
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iOS-native mobile web UX rules. Use when building any UI component, fixing mobile issues, reviewing responsive code, or touching viewport heights (dvh vs h-screen), safe areas, Dialog vs Drawer, tabs on mobile, touch targets, or input zoom.
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Create a new find-XXXX preprocessor Python script from scratch (no existing SKILL.md), add configs/<GAMEVER>.yaml skill and symbol entries. Covers xref-string-based and LLM_DECOMPILE-based discovery patterns. Use when a GitHub issue or user instruction specifies a new function to find.
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