2,719 件 ・ 関連度順
概要と使いどころ
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, generating bootstrap consensus, or needing quick exploratory phylogenies before running full ML analysis.
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Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.
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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.
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Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.
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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.
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Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.
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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.
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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.
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Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
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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.
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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).
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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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Python-first workflow for bulk RNA-seq expression intake, normalization, sample QC, and downstream-ready matrices.
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Migrate Rust TUIs from ratatui (or cursive, Python textual) to SuperLightTUI v0.23. Use when porting an existing TUI codebase to SLT, or when the user asks "how do I do X from ratatui in SLT". Korean triggers "ratatui 마이그레이션", "SLT로 포팅", "이걸 SLT로".
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Migrate Rust TUIs from ratatui (or cursive, Python textual) to SuperLightTUI v0.20. Use when porting an existing TUI codebase to SLT, or when the user asks "how do I do X from ratatui in SLT". Korean triggers "ratatui 마이그레이션", "SLT로 포팅", "이걸 SLT로".
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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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Create and manage test data with factory patterns, fixture strategies, data anonymization, and synthetic data generation. Covers Fishery (TypeScript), FactoryBot (Ruby), Factory Boy (Python), database seeding, cleanup strategies, and GDPR-compliant data handling. Use when: "test data," "fixtures," "factories," "seed data," "synthetic data," "test database," "data anonymization." Not for: migration/integrity testing of the DB itself — use database-testing; environment provisioning and database branching strategy — use test-environments. Related: test-environments, database-testing, api-testing, unit-testing.
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Generate realistic speech with the ElevenLabs API and its Python and Node.js SDKs. Use when a user asks to convert text to speech, stream audio, clone a voice, pick a TTS model, or build a voice agent with ElevenLabs.
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direnv loads and unloads environment variables automatically when you enter and leave a directory, using a per-project .envrc file. Use when a user asks to manage env vars per project, auto-switch configs, avoid manually sourcing .env files, set up .envrc, use dotenv with direnv, or pick a Python or Node version per directory.
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E2B is a cloud platform that gives AI agents secure, isolated sandboxes — ephemeral Linux VMs with a filesystem, package managers, and internet access — to run AI-generated code safely. Use when a user wants an agent to execute Python or JavaScript, install packages, read/write files, or run a long process without risking the host machine, or wants to wire code execution into a LangChain, CrewAI, or custom agent loop.
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Write CI/CD pipelines as code with Dagger — portable, cacheable, container-based pipelines that run locally and in any CI system. Use when someone asks to "write CI pipeline in TypeScript", "portable CI/CD", "run GitHub Actions locally", "Dagger pipeline", "CI as code", "containerized build pipeline", or "test my CI locally before pushing". Covers Dagger SDK (TypeScript/Python), pipeline composition, caching, secrets, and multi-stage builds.
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Dagster is a data pipeline orchestrator built around the concept of software-defined assets. Learn to define assets, ops, jobs, schedules, sensors, and resources for building maintainable data platforms.
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Transcribes and analyzes speech with the Deepgram API: pre-recorded audio, real-time streaming, text-to-speech and voice agents. Use when a user asks to convert speech to text, implement real-time transcription, add speaker labels or summaries to a recording, detect languages, build a voice agent with turn detection, or integrate Deepgram SDKs (JavaScript or Python).
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You are an expert in Crawl4AI, the open-source web crawler built for AI applications. You help developers extract clean, structured data from websites for LLM training, RAG pipelines, and content analysis — with automatic markdown conversion, JavaScript rendering, CSS-based extraction, LLM-powered structured extraction, and session management for multi-page crawling.
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