Lamindb

This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies. Part of the AlterLab Academic Skills suite.

Guidance for open science practices -- preregistration, open data, reproducible analysis, open access publishing, and FAIR principles. Part of the AlterLab Academic Skills suite.

当需要用 lark-cli 操作飞书多维表格（Base）时调用：搜索 Base、建表、字段管理、记录读写、记录分享链接、视图配置、历史查询，以及角色/表单/仪表盘管理/工作流；也适用于把旧的 +table / +field / +record 写法改成当前命令写法。涉及字段设计、公式字段、查找引用、跨表计算、行级派生指标、数据分析需求时也必须使用本 skill。

Hugging Face Hub CLI (`hf`) for downloading, uploading, and managing models, datasets, spaces, buckets, repos, papers, jobs, and more on the Hugging Face Hub. Use when: handling authentication; managing local cache; managing Hugging Face Buckets; running or scheduling jobs on Hugging Face infrastructure; managing Hugging Face repos; discussions and pull requests; browsing models, datasets and spaces; reading, searching, or browsing academic papers; managing collections; querying datasets; configuring spaces; setting up webhooks; or deploying and managing HF Inference Endpoints. Make sure to use this skill whenever the user mentions 'hf', 'huggingface', 'Hugging Face', 'huggingface-cli', or 'hugging face cli', or wants to do anything related to the Hugging Face ecosystem and to AI and ML in general. Also use for cloud storage needs like training checkpoints, data pipelines, or agent traces. Use even if the user doesn't explicitly ask for a CLI command. Replaces the deprecated `huggingface-cli`.

Creates, manages, and queries Arize datasets and examples. Covers dataset CRUD, appending examples, exporting data, and file-based dataset creation using the ax CLI. Use when the user needs test data, evaluation examples, or mentions create dataset, list datasets, export dataset, append examples, dataset version, golden dataset, or test set.

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.