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Found 56 Skills
Comprehensive epigenomics and gene regulation analysis integrating ENCODE functional genomics data, JASPAR transcription factor binding motifs, SCREEN cis-regulatory elements, ReMap TF binding sites, RegulomeDB variant regulatory scoring, 4D Nucleome chromatin conformation, and Ensembl regulatory features. Performs regulatory element cataloging, transcription factor analysis, variant regulatory impact scoring, chromatin conformation mapping, and gene-centric regulatory landscape profiling. Use when asked about gene regulation, enhancers, promoters, transcription factor binding, epigenetic modifications, chromatin structure, regulatory variants, or non-coding genome function.
Take a PRD and build a dark factory around it - a repository that takes work in as an issue and ships validated code out with nobody at the keyboard - one component at a time, into the user's actual repo. Covers the five components in construction order - the guidance layer, the validation harness, the workflow-driven repo, deployment, and the trigger that makes it autonomous - and is agnostic about which coding agent runs underneath (Claude Code, Codex, Archon, the Agent SDK, Cline, Goose, Amp, Pi). It encodes the AI coding process the user already runs rather than replacing it. Requires a PRD as input and deliberately does not write one. Use when the user wants to build a dark factory, an autonomous or self-driving repository, a software factory, an agent that ships its own code, an unattended or overnight coding loop, or asks how to get to level 4 or level 5 of AI coding autonomy; and when they mention dark factory, lights-out coding, autonomous PRs, or a repo that maintains itself.
Apply when writing stateful logic, or when code branches a lot or repeats a shape assumption across files. Encode the domain in a structure instead of scattered conditionals.
Scan how you actually work with your coding agent and surface what to encode next. Point it at ONE run's artifacts to find what would have prevented a specific failure (the reactive loop — 'that went wrong, what should change in the AI layer?'), or at a window of session logs to find recurring patterns worth building (the proactive scan). Agent-agnostic. Outputs a shape-only HTML report. Use to evolve your system from real usage.
This skill should be used when the user asks anything about Adobe After Effects — to "write an After Effects expression", "make a wiggle / loopOut / inertial bounce", "rig a control with a slider / null", "build a MOGRT / Essential Graphics template", "export AE to Lottie or Media Encoder"; OR to "export from After Effects", "export with transparency / an alpha channel", "fix a black background on export", "choose ProRes vs H.264", "which codec / what bitrate for 1080p / 4K", "stop H.264 disappearing from the Render Queue"; OR when "After Effects is slow / laggy / crashing / froze", "RAM preview won't play in real time", "AE is using all my memory / render takes forever", "how do I speed up After Effects"; OR to "organize my After Effects project", "relink missing footage", "fix broken links after moving files", "set a folder structure / naming conventions", "batch rename layers", or "write an ExtendScript / .jsx script". Covers expressions & rigging, export recipes, performance triage, and project hygiene.
Use when writing, reviewing, or refactoring code, or scaffolding a new project. Language-agnostic principles (types encode invariants, parse don't validate, errors as values, no mocks, earn abstractions) with dialects for Rust, TypeScript, Go, and Python.
Adaptive PLAN.md executor that preserves cook-quality implementation while choosing between direct main-agent work and sub-agent delegation. Runs a phase directly through cook when delegation has no material parallelism, context, or capability benefit; otherwise dispatches disjoint assignments through encode-agent prompts, discloses agent type, model, effort, scope, and rationale before each dispatch, and acceptance-reviews every returned diff. Expects prep to have created PLAN.md + HANDOFF.md and composes with cook, encode-agent, encode-docs, and handoff. Triggers: "/cater".
Investigate transcription factor binding, cis-regulatory elements, chromatin accessibility, and regulatory variant annotation. Use when asked about TF binding sites, enhancers, promoters, ChIP-seq data, ATAC-seq signals, candidate cis-regulatory elements (cCREs), or the regulatory impact of genomic variants.