[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M77Y5K7VCKGD3RBZ53XCDQ09":3,"skill-same:01M77Y5K7VCKGD3RBZ53XCDQ09":49},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":18,"publishedAt":19,"linkOnly":20,"markdownContent":21,"markdownBody":22,"frontMatter":23,"refName":26,"commitSha":27,"skillDirectory":28,"forksCount":29,"repositoryHtmlUrl":30,"repositoryHomepageUrl":6,"ownerHtmlUrl":31,"ownerBlogUrl":32,"ownerDescription":33,"updatedAt":34,"install":35,"resources":48},"01M77Y5K7VCKGD3RBZ53XCDQ09","gget",null,"gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.","503496348-ops\u002Fmischief-production","503496348-ops","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F266905914?v=4","01M77X5J7XQWWZGT8998HDGXQM","AtomCollide","01M77X5J8V78Y3NXMY6BBC75X9",2,"MIT","https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production\u002Fblob\u002Fmain\u002Fskills\u002Fecc-scientific-pkg-gget\u002FSKILL.md",[],[],"2026-11-15 14:19:17",false,"---\nname: gget\ndescription: gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.\nmetadata:\n  origin: community\n---\n\n# gget\n\nUse this skill when a task needs quick bioinformatics lookup across genomic\nreference databases with the `gget` CLI or Python package.\n\n## When to Use\n\n- Finding Ensembl IDs, gene metadata, transcript details, or sequences.\n- Running quick BLAST or BLAT lookups without building a full local pipeline.\n- Fetching reference genome links and annotations from Ensembl.\n- Querying protein structure, pathway, cancer, expression, or disease-association\n  modules through a single interface.\n- Creating a reproducible first-pass evidence log before moving to heavier\n  tools such as Biopython, Snakemake, Nextflow, BLAST+, or database-specific\n  clients.\n\nUse a dedicated workflow instead of `gget` when the task requires regulated\nclinical interpretation, high-throughput production pipelines, or fine-grained\ncontrol over database versions and local indexes.\n\n## Installation\n\nUse a clean Python environment.\n\n```bash\npython -m venv .venv\n. .venv\u002Fbin\u002Factivate\npython -m pip install --upgrade pip\npython -m pip install --upgrade gget\ngget --help\n```\n\nIf `uv` is available:\n\n```bash\nuv venv\n. .venv\u002Fbin\u002Factivate\nuv pip install gget\n```\n\nBefore relying on an older environment, upgrade `gget` and re-check the module\ndocs. The upstream databases queried by `gget` change over time.\n\n## Basic Patterns\n\nCLI shape:\n\n```bash\ngget \u003Cmodule> [arguments] [options]\n```\n\nPython shape:\n\n```python\nimport gget\n\nresult = gget.search([\"BRCA1\"], species=\"human\")\nprint(result)\n```\n\nCommon workflow:\n\n1. Identify the species, assembly, gene ID type, and database needed.\n2. Check the current module documentation for arguments.\n3. Run a small query first.\n4. Save output with an explicit filename and date.\n5. Record module name, version, arguments, and database assumptions.\n\n## Common Modules\n\nUse current upstream docs for exact arguments. These modules are common first\nchoices:\n\n- `gget search`: find Ensembl IDs from search terms.\n- `gget info`: retrieve metadata for Ensembl, UniProt, or related IDs.\n- `gget seq`: fetch nucleotide or amino-acid sequences.\n- `gget ref`: retrieve reference genome download links.\n- `gget blast`: run a quick BLAST query.\n- `gget blat`: locate a sequence against supported genome assemblies.\n- `gget muscle`: run multiple sequence alignment.\n- `gget diamond`: run local sequence alignment against reference sequences.\n- `gget alphafold` and `gget pdb`: inspect protein-structure references.\n- `gget enrichr`, `gget opentargets`, `gget archs4`, `gget bgee`, `gget cbio`,\n  and `gget cosmic`: explore enrichment, target, expression, cancer, and disease\n  association data.\n\nDo not assume every module supports every Python version or dependency set.\nSome optional scientific dependencies have narrower version support than the\ncore package.\n\n## Quick Examples\n\nFind genes:\n\n```bash\ngget search -s human brca1 dna repair -o brca1-search.json\n```\n\nFetch gene metadata:\n\n```bash\ngget info ENSG00000012048 -o brca1-info.json\n```\n\nFetch a sequence:\n\n```bash\ngget seq ENSG00000012048 -o brca1-seq.fa\n```\n\nRun a small BLAST query:\n\n```bash\ngget blast \"MEEPQSDPSVEPPLSQETFSDLWKLLPEN\" -l 10 -o blast-results.json\n```\n\nPython example:\n\n```python\nimport gget\n\ngenes = gget.search([\"BRCA1\", \"DNA repair\"], species=\"human\")\ninfo = gget.info([\"ENSG00000012048\"])\nsequence = gget.seq(\"ENSG00000012048\")\n```\n\n## Reproducibility Log\n\nFor scientific outputs, include enough metadata to replay the query.\n\n```markdown\n| Date | gget version | Module | Query | Species\u002Fassembly | Output | Notes |\n| --- | --- | --- | --- | --- | --- | --- |\n| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | Docs checked before run |\n```\n\nAlso record:\n\n- Python version and environment manager.\n- Any optional dependency installed through `gget setup`.\n- Database-specific identifiers returned by the query.\n- Whether output is JSON, CSV, FASTA, or a DataFrame export.\n- Any failures that were resolved by upgrading `gget`.\n\n## Review Checklist\n\n- Did you upgrade or verify the installed `gget` version?\n- Did you check the current upstream module docs before using arguments?\n- Is the species or assembly explicit?\n- Are identifiers preserved exactly, including Ensembl\u002FUniProt prefixes?\n- Is the result labeled as database output rather than clinical interpretation?\n- Is the query reproducible from the saved command or Python snippet?\n- Are optional dependencies installed in an isolated environment?\n\n## References\n\n- [gget documentation](https:\u002F\u002Fpachterlab.github.io\u002Fgget\u002F)\n- [gget updates](https:\u002F\u002Fpachterlab.github.io\u002Fgget\u002Fen\u002Fupdates.html)\n- [gget GitHub repository](https:\u002F\u002Fgithub.com\u002Fpachterlab\u002Fgget)\n- [gget Bioinformatics paper](https:\u002F\u002Fdoi.org\u002F10.1093\u002Fbioinformatics\u002Fbtac836)\n","# gget\n\nUse this skill when a task needs quick bioinformatics lookup across genomic\nreference databases with the `gget` CLI or Python package.\n\n## When to Use\n\n- Finding Ensembl IDs, gene metadata, transcript details, or sequences.\n- Running quick BLAST or BLAT lookups without building a full local pipeline.\n- Fetching reference genome links and annotations from Ensembl.\n- Querying protein structure, pathway, cancer, expression, or disease-association\n  modules through a single interface.\n- Creating a reproducible first-pass evidence log before moving to heavier\n  tools such as Biopython, Snakemake, Nextflow, BLAST+, or database-specific\n  clients.\n\nUse a dedicated workflow instead of `gget` when the task requires regulated\nclinical interpretation, high-throughput production pipelines, or fine-grained\ncontrol over database versions and local indexes.\n\n## Installation\n\nUse a clean Python environment.\n\n```bash\npython -m venv .venv\n. .venv\u002Fbin\u002Factivate\npython -m pip install --upgrade pip\npython -m pip install --upgrade gget\ngget --help\n```\n\nIf `uv` is available:\n\n```bash\nuv venv\n. .venv\u002Fbin\u002Factivate\nuv pip install gget\n```\n\nBefore relying on an older environment, upgrade `gget` and re-check the module\ndocs. The upstream databases queried by `gget` change over time.\n\n## Basic Patterns\n\nCLI shape:\n\n```bash\ngget \u003Cmodule> [arguments] [options]\n```\n\nPython shape:\n\n```python\nimport gget\n\nresult = gget.search([\"BRCA1\"], species=\"human\")\nprint(result)\n```\n\nCommon workflow:\n\n1. Identify the species, assembly, gene ID type, and database needed.\n2. Check the current module documentation for arguments.\n3. Run a small query first.\n4. Save output with an explicit filename and date.\n5. Record module name, version, arguments, and database assumptions.\n\n## Common Modules\n\nUse current upstream docs for exact arguments. These modules are common first\nchoices:\n\n- `gget search`: find Ensembl IDs from search terms.\n- `gget info`: retrieve metadata for Ensembl, UniProt, or related IDs.\n- `gget seq`: fetch nucleotide or amino-acid sequences.\n- `gget ref`: retrieve reference genome download links.\n- `gget blast`: run a quick BLAST query.\n- `gget blat`: locate a sequence against supported genome assemblies.\n- `gget muscle`: run multiple sequence alignment.\n- `gget diamond`: run local sequence alignment against reference sequences.\n- `gget alphafold` and `gget pdb`: inspect protein-structure references.\n- `gget enrichr`, `gget opentargets`, `gget archs4`, `gget bgee`, `gget cbio`,\n  and `gget cosmic`: explore enrichment, target, expression, cancer, and disease\n  association data.\n\nDo not assume every module supports every Python version or dependency set.\nSome optional scientific dependencies have narrower version support than the\ncore package.\n\n## Quick Examples\n\nFind genes:\n\n```bash\ngget search -s human brca1 dna repair -o brca1-search.json\n```\n\nFetch gene metadata:\n\n```bash\ngget info ENSG00000012048 -o brca1-info.json\n```\n\nFetch a sequence:\n\n```bash\ngget seq ENSG00000012048 -o brca1-seq.fa\n```\n\nRun a small BLAST query:\n\n```bash\ngget blast \"MEEPQSDPSVEPPLSQETFSDLWKLLPEN\" -l 10 -o blast-results.json\n```\n\nPython example:\n\n```python\nimport gget\n\ngenes = gget.search([\"BRCA1\", \"DNA repair\"], species=\"human\")\ninfo = gget.info([\"ENSG00000012048\"])\nsequence = gget.seq(\"ENSG00000012048\")\n```\n\n## Reproducibility Log\n\nFor scientific outputs, include enough metadata to replay the query.\n\n```markdown\n| Date | gget version | Module | Query | Species\u002Fassembly | Output | Notes |\n| --- | --- | --- | --- | --- | --- | --- |\n| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | Docs checked before run |\n```\n\nAlso record:\n\n- Python version and environment manager.\n- Any optional dependency installed through `gget setup`.\n- Database-specific identifiers returned by the query.\n- Whether output is JSON, CSV, FASTA, or a DataFrame export.\n- Any failures that were resolved by upgrading `gget`.\n\n## Review Checklist\n\n- Did you upgrade or verify the installed `gget` version?\n- Did you check the current upstream module docs before using arguments?\n- Is the species or assembly explicit?\n- Are identifiers preserved exactly, including Ensembl\u002FUniProt prefixes?\n- Is the result labeled as database output rather than clinical interpretation?\n- Is the query reproducible from the saved command or Python snippet?\n- Are optional dependencies installed in an isolated environment?\n\n## References\n\n- [gget documentation](https:\u002F\u002Fpachterlab.github.io\u002Fgget\u002F)\n- [gget updates](https:\u002F\u002Fpachterlab.github.io\u002Fgget\u002Fen\u002Fupdates.html)\n- [gget GitHub repository](https:\u002F\u002Fgithub.com\u002Fpachterlab\u002Fgget)\n- [gget Bioinformatics paper](https:\u002F\u002Fdoi.org\u002F10.1093\u002Fbioinformatics\u002Fbtac836)\n",{"name":5,"metadata":24,"description":7},{"origin":25},"community","main","c9103dbad48ef3005f163584d0f2abd4591217f6","skills\u002Fecc-scientific-pkg-gget",1,"https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production","https:\u002F\u002Fgithub.com\u002F503496348-ops","https:\u002F\u002F503496348-ops.github.io\u002Fatomcollide-product-matrix\u002F#tree","元素碰撞-AtomCollide-AI 智能体实验室 测试人专属成长社群 正式招募\r\n我们的目标很纯粹：连接每一位测试工程师\u002FAI使用探索与爱好者，让你在这里既能扎实打磨技术硬实力，也能打通职业晋升的新通路，这是一个专注于AI领域的开源组","2026-07-30 00:35:42",{"source":8,"skillName":5,"commands":36,"prompt":46,"zipAvailable":47},[37,40,43],{"tool":38,"command":39},"npx","npx skills add 503496348-ops\u002Fmischief-production --skill gget",{"tool":41,"command":42},"bunx","bunx skills add 503496348-ops\u002Fmischief-production --skill gget",{"tool":44,"command":45},"pnpm","pnpm dlx skills add 503496348-ops\u002Fmischief-production --skill gget","安装技能，技能地址：https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production\u002Fblob\u002Fmain\u002Fskills\u002Fecc-scientific-pkg-gget\u002FSKILL.md",true,[],[50,57,64,71,78,85],{"skillNo":51,"name":52,"nameZh":6,"description":53,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":54,"categories":55,"keywords":56,"publishedAt":19},"01M77YG7NPZHE751W9QGK3H9ED","writing-skills","Use when creating new skills, editing existing skills, or verifying skills work before deployment","https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production\u002Fblob\u002Fmain\u002Fskills\u002Fsp-writing-skills\u002FSKILL.md",[],[],{"skillNo":58,"name":59,"nameZh":6,"description":60,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":61,"categories":62,"keywords":63,"publishedAt":19},"01M77YG4HPYH0GJP974DZ6KCPQ","writing-plans","Use when you have a spec or requirements for a multi-step task, before touching code","https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production\u002Fblob\u002Fmain\u002Fskills\u002Fsp-writing-plans\u002FSKILL.md",[],[],{"skillNo":65,"name":66,"nameZh":6,"description":67,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":68,"categories":69,"keywords":70,"publishedAt":19},"01M77YFZW1FZ1GVC5C89NPE5M8","verification-before-completion","Use when about to claim work is complete, fixed, or passing, before committing or creating PRs - requires running verification commands and confirming output before making any success claims; evidence before assertions always","https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production\u002Fblob\u002Fmain\u002Fskills\u002Fsp-verification-before-completion\u002FSKILL.md",[],[],{"skillNo":72,"name":73,"nameZh":6,"description":74,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":75,"categories":76,"keywords":77,"publishedAt":19},"01M77YFVPWANT5VE5GWBTKHPA2","using-智械工程","Use when starting any conversation - establishes how to find and use skills, requiring skill invocation before ANY response including clarifying questions","https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production\u002Fblob\u002Fmain\u002Fskills\u002Fsp-using-superpowers\u002FSKILL.md",[],[],{"skillNo":79,"name":80,"nameZh":6,"description":81,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":82,"categories":83,"keywords":84,"publishedAt":19},"01M77YFQJAW5PX3QYSBCD3B24S","using-git-worktrees","Use when starting feature work that needs isolation from current workspace or before executing implementation plans - ensures an isolated workspace exists via native tools or git worktree fallback","https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production\u002Fblob\u002Fmain\u002Fskills\u002Fsp-using-git-worktrees\u002FSKILL.md",[],[],{"skillNo":86,"name":87,"nameZh":6,"description":88,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":89,"categories":90,"keywords":91,"publishedAt":19},"01M77YFMSTB70VX8W2QHNJWYB0","test-driven-development","Use when implementing any feature or bugfix, before writing implementation code","https:\u002F\u002Fgithub.com\u002F503496348-ops\u002Fmischief-production\u002Fblob\u002Fmain\u002Fskills\u002Fsp-test-driven-development\u002FSKILL.md",[],[]]