Results for “python”

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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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.

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Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.

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Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Use when running analytical SQL over Parquet/CSV/JSON without a warehouse, replacing pandas for data wrangling, joining S3 data in-place, building local data marts, or embedding OLAP into an app. Triggers: read_parquet/read_csv setup, partitioned dataset queries, hive partitioning, glob patterns for S3, COPY TO export, attach Postgres/MySQL, UDFs in Python/R, MotherDuck cloud sync, columnar performance vs row stores. NOT for OLTP workloads (concurrent writes), distributed analytics at petabyte scale (use Spark/Trino), or vector search (use pgvector/Lance).

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Design error handling strategies for TypeScript and Python applications — exception hierarchies, Result/Either types, retry patterns, error boundaries, and structured error logging. Use when designing error handling architecture, choosing between exceptions and Result types, implementing retry logic, or building error recovery flows. Activate on "error handling", "exception hierarchy", "Result type", "retry pattern", "circuit breaker", "error boundary", "Pokemon exception". NOT for debugging specific runtime errors, logging infrastructure setup, or monitoring/alerting configuration.

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Chooses and designs developer surfaces for an agentic product: SDK, CLI, MCP, GUI, API, webhooks, and pd tube-style listener/sender workflows. Use when deciding why a user belongs in an SDK versus CLI/MCP/GUI, planning Python SDK parity, or making agent invocation easy across languages. NOT for implementing the full SDK, generic API docs, or UI visual design.

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Send and receive transactional emails with Cloudflare Email Service (Email Sending + Email Routing). Use when building email sending (Workers binding or REST API), email routing, Agents SDK email handling, or integrating email into any app — Workers, Node.js, Python, Go, etc. Also use for email deliverability, SPF/DKIM/DMARC, wrangler email setup, MCP email tools, or when a coding agent needs to send emails. Even for simple requests like "add email to my Worker" — this skill has critical config details.

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Expert bot developer specializing in Discord, Telegram, Slack automation with deep knowledge of rate limiting, state machines, event sourcing, moderation systems, and conversational AI integration. Activate on 'Discord bot', 'Telegram bot', 'Slack bot', 'chat automation', 'moderation system'. NOT for web APIs (use backend-architect), general automation scripts (use python-pro), or frontend chat widgets (use frontend-developer).

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Convert an existing find-XXXX SKILL.md into a preprocessor Python script, updating configs/<GAMEVER>.yaml and removing the old SKILL.md. Covers xref-string-based and LLM_DECOMPILE-based discovery patterns.

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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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Perform language and framework specific security best-practice reviews and suggest improvements. Use when the user explicitly requests security best practices guidance, a security review/report, or secure-by-default coding help. Trigger only for supported languages (python, javascript/typescript, go), and not for general debugging or non-security tasks.

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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Build a LiveAvatar integration end-to-end — assesses the user's existing stack, recommends the optimal path, and guides implementation. Use when: (1) Building a new LiveAvatar integration, (2) Adding a real-time avatar to an app or site, (3) Connecting LiveAvatar to an existing AI pipeline, (4) User mentions LiveAvatar, real-time avatar, interactive avatar, conversational avatar, or lip-sync avatar, (5) Deciding between Embed, FULL Mode, and LITE Mode, (6) Migrating from HeyGen Interactive Avatar to LiveAvatar.

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Troubleshoot and debug LiveAvatar integration issues. Use when the user's LiveAvatar integration isn't working, the avatar is silent, audio is garbled, sessions fail to start, events aren't received, or they're getting API errors.

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Build voice AI agents with LiveKit Cloud and the Agents SDK. Use when the user asks to "build a voice agent", "create a LiveKit agent", "add voice AI", "implement handoffs", "structure agent workflows", or is working with LiveKit Agents SDK. Provides opinionated guidance for the recommended path: LiveKit Cloud + LiveKit Inference. REQUIRES writing tests for all implementations.

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Collect and submit developer feedback to the LiveAvatar team. Use when: (1) A LiveAvatar integration is done, working, finished, or complete, (2) The user says "it works", "we're done", "that's it", "ship it", (3) The user is frustrated, stuck, or giving up — "this is broken", "this doesn't work", "I'm stuck", "I give up", "this is frustrating", "I want to report an issue", (4) The user explicitly asks to give feedback, report a bug, file an issue, or share a suggestion about LiveAvatar, (5) You've seen 3+ failed attempts at the same integration step, (6) You just finished writing or generating LiveAvatar integration code for the user.

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Answers plain-word questions from a repo's CSV, JSON, Parquet and YAML files, or a .duckdb file, with DuckDB, and shows the SQL it ran. Read-only. Trigger to query, count, join, filter or summarise data files, including analytics CSVs exported from a video platform; to build a Parquet or DuckDB cache; to check no .duckdb, .wal or .parquet cache is committed or stale; when a query hits a locked database file; or say duckrunner (ask, cache, check, refresh). Needs the user-installed duckdb Python package; never a database server. DuckDB docs, S3 and MotherDuck are the duckdb-skills plugin's; outside research researchscribe's.

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Drives OBS Studio through its WebSocket, read-only by default, and turns recordings into clips, VOD cuts and chapters with FFmpeg. Trigger to audit an OBS setup; when a stream drops frames or lags; to switch a scene, mark a moment or save the replay buffer; to cut clips, burn in captions, normalize loudness or write chapters; when OBS shares a GPU; or say obsrunner (audit, check, set, mark, post, sheet, status, hold, release, refresh). Live work needs the user-installed obsws-python package. Never goes live, uploads or moderates chat. Caption files are whisperrunner's; thumbnails comfyrunner's; titles commscribe's; analytics duckrunner's.

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Runs the test-first build loop (spec, plan, thin slices, failing test first, verify, commit) for a Godot 4 game in GDScript or C# first; in a TypeScript, Python or other repo when test-first, slices or a reproduce-first fix is asked for. Trigger to build or add a game feature, mechanic, stat, system or milestone, even when told to test later; to turn a spec or grill record into slices; to fix a game bug from a reproduction, one hypothesis at a time; on "write the test first", "what's the next slice", "is this slice done" or "is this milestone ready to exit"; or say slicesmith (spec, plan, slice, fix, exit). Run proof and gate rulings are godotsmith's; diff review a review tool's; repo maps researchscribe's; art pixelsmith's; audio soundsmith's; interviews grillwright's; fan-out dispatchwright's.

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Elite UX/UI & Advanced GSAP Motion Engineer. Enforces Python-driven true randomization for layout variance, strict AIDA page structure, wide editorial typography (bans 6-line wraps), gapless bento grids, strict GSAP ScrollTriggers (pinning, stacking, scrubbing), inline micro-images, and massive section spacing.

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SDK installation and setup patterns for Agent-to-Agent Protocol across Python, TypeScript, Java, C#, and Go. Use when implementing A2A protocol, setting up SDKs, configuring authentication, or when user mentions SDK installation, language-specific setup, or A2A integration.

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Master skill for Abaqus FEA scripting. Use for any finite element analysis, topology optimization, or Abaqus Python scripting task. Routes to appropriate specialized skills.

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