> ## Documentation Index > Fetch the complete documentation index at: https://wiki.latch.bio/llms.txt > Use this file to discover all available pages before exploring further. # Skills > Built-in technology skills and custom skills from private GitHub repositories. Skills are prompt packages that teach the agent new capabilities — domain-specific workflows, analysis templates, institutional conventions, or technology-specific guidance. Each skill is a directory with a `SKILL.md` entrypoint that the agent loads on demand based on context. ## Developing Skills (Branch Workflow) You can test skill changes on a branch before merging to `main` by pinning a notebook to a specific `latch-skills` branch. Push a branch to the [`latch-skills`](https://github.com/latchbio/latch-skills) repository with your changes (new or modified skills). In **Edit** mode, open **Runtime Settings** (via the runtime dropdown in the notebook top bar) and select your branch from the **Skills Branch** picker. Restart the notebook runtime. On startup, the agent clones `latch-skills` at your chosen branch instead of `main`. Send a prompt that should trigger your skill. Verify the agent loads and uses it correctly. Once verified, merge your branch into `main`. Clear the Skills Branch setting (or leave it as default) so the notebook tracks `main` going forward. The skills branch setting is per-notebook and persists across restarts. On every restart, the runtime fetches the latest commit on the configured branch, so you can push updates and restart without changing the setting. ## Built-in Skills Every agent session includes Latch's public skill set from [`latch-skills`](https://github.com/latchbio/latch-skills). These are cloned automatically at startup — no registration required. By default, the `main` branch is used. See [Developing Skills](#developing-skills-branch-workflow) above to test on a different branch. ### Platform Skills Core Latch Plots APIs and patterns: | Skill | Description | | ------------------- | -------------------------------------------------------------------------------------------------------------------------------- | | `latch-plots-ui` | Widget APIs for output (plots, tables, H5 viewers), user input (selects, sliders, checkboxes), and layout (rows, columns, grids) | | `latch-data-access` | File selection widgets, Latch Data browsing, Registry tables, and LPath utilities for `latch://` paths | | `latch-workflows` | Launching and monitoring bioinformatics workflows — parameter construction, validation, and output retrieval | | `latch-curation` | Curating external datasets (GEO/GSE) into Latch-compatible AnnData with Ensembl gene IDs and ontology-annotated metadata | ### Technology Skills Provider-specific analysis workflows and best practices: | Skill | Technology | Description | | --------------- | ----------------------- | ---------------------------------------------------------------------------------------------------- | | `takara-devkit` | Takara Seeker / Trekker | QC, background removal, normalization, clustering, differential expression, and cell typing | | `xenium-devkit` | 10x Xenium | Data preparation, preprocessing, differential expression, cell type annotation, and domain detection | | `vizgen-devkit` | Vizgen MERFISH | Cell segmentation, preprocessing, QC, spatial analysis, and secondary analysis | | `atlasx-devkit` | AtlasXomics DBiT-seq | QC, clustering, differential analysis, and cell type annotation for spatial ATAC-seq | ## Custom Skills Organization admins can register private GitHub repositories containing custom skills that get loaded into agent runtimes across all workspaces in the organization. ## Skill Repository Structure A skill repository must follow this structure: ``` my-org-skills/ ├── README.md # For humans browsing GitHub (not loaded by agent) │ ├── spatial-analysis/ # Each top-level directory = one skill │ ├── SKILL.md # Required: skill entrypoint │ ├── reference.md # Optional: supporting documentation │ └── examples/ │ └── xenium-workflow.md # Optional: example outputs │ ├── curation/ │ ├── SKILL.md │ ├── steps/ │ │ ├── harmonize.md │ │ └── download.md │ └── scripts/ │ └── validate.py # Optional: scripts the agent can execute │ └── volcano-plot/ ├── SKILL.md └── templates/ └── template.md # Optional: templates for the agent to fill in ``` ### Rules * Each top-level directory containing a `SKILL.md` file becomes a skill * Only one level of skill directories — no nesting skills inside skills * `README.md` at the repo root is for GitHub — the agent does not load it * Skill directory names must be **unique across all registered repos** in an organization. If two repos define the same skill name, syncing will fail. ## Writing a SKILL.md Every skill needs a `SKILL.md` file with YAML frontmatter and markdown instructions: ```yaml theme={null} --- name: spatial-analysis description: > Spatial transcriptomics analysis workflows. Use when the user is working with Xenium, Visium, or MERFISH data and needs help with spatial analysis, neighborhood detection, or co-expression. --- When performing spatial analysis: 1. Identify the technology platform from the data 2. Load the appropriate reference panel 3. Follow the platform-specific QC workflow 4. Generate spatial plots with appropriate coloring For detailed API usage, see [reference.md](reference.md). ``` ### Required Fields | Field | Description | | ------------- | ------------------------------------------------------------------------------------------------------------ | | `name` | Lowercase letters, numbers, and hyphens only (max 64 characters). Used as the skill identifier. | | `description` | What the skill does and when to use it. The agent reads this to decide when to load the skill automatically. | ### Optional Fields | Field | Description | | -------------------------- | ---------------------------------------------------------------------------------- | | `allowed-tools` | Restrict which tools the agent can use (e.g., `Read, Grep, Glob`). | | `disable-model-invocation` | Set to `true` to prevent auto-loading. The skill can only be triggered explicitly. | | `argument-hint` | Hint shown for expected arguments (e.g., `[dataset-name]`). | ### Supporting Files Keep `SKILL.md` focused and under 500 lines. Move detailed reference material to separate files and link them from `SKILL.md`: ```markdown theme={null} ## Additional resources - For complete API details, see [reference.md](reference.md) - For usage examples, see [examples/](examples/) ``` The agent loads supporting files on demand when it follows a link from `SKILL.md`. ## Merging Multiple Repositories When multiple repositories are registered with the same target path (the default `.claude/skills/`), their skill directories are merged side by side: ``` .claude/skills/ ├── xenium-qc/ # from repo A ├── lab-conventions/ # from repo A ├── my-custom-plots/ # from repo B └── curation/ # from repo B ``` Skill directory names must be unique across all repos. If two repos both define a `spatial-analysis/` skill, syncing will fail and the conflict will be reported in **Organization Settings → Agent Skills**. ## Registering a Repository Generate a [GitHub PAT](https://github.com/settings/tokens) with **repo** scope so the agent runtime can clone private repositories. Go to **Organization Settings → Agent Skills → GitHub Authentication** and enter your GitHub username and token. Click **Add Repository** and provide: * **Display Name**: A human-readable label (e.g., "Our Lab Skills") * **Repository URL**: The HTTPS clone URL (e.g., `https://github.com/my-org/agent-skills.git`) * **Branch**: The branch to track (defaults to `main`) * **Target Path**: Where to mount in the runtime (defaults to `.claude/skills`) When a new workspace agent session starts, the registered repositories are cloned into the runtime. The agent discovers all skills automatically. ## How Skills Are Loaded When an agent runtime starts in a workspace belonging to your organization: 1. All registered repositories are cloned using the org's GitHub PAT 2. Skill directory names are checked for uniqueness — conflicts block the sync 3. The agent discovers `SKILL.md` files and reads their `description` fields 4. During a session, the agent automatically loads a skill when your request matches its description Skills do not need to be invoked explicitly — the agent decides when they are relevant based on the conversation. ## Example: Technology-Specific Skill ```yaml theme={null} --- name: xenium-qc description: > Xenium spatial transcriptomics QC workflow. Use when the user has Xenium data and needs quality control, transcript filtering, or cell segmentation validation. --- ## Xenium QC Workflow 1. Load the Xenium output bundle with `xeniumranger` 2. Check transcript counts per cell (expect >50 median) 3. Validate cell segmentation boundaries 4. Filter low-quality cells (< 20 transcripts) 5. Generate spatial QC plots For platform-specific thresholds, see [reference.md](reference.md). ``` ## Example: Institutional Conventions Skill ```yaml theme={null} --- name: lab-conventions description: > Lab-specific analysis conventions and standards. Use when generating plots, writing methods sections, or exporting results. --- ## Plot Standards - Use colorblind-safe palettes (viridis, cividis) - Font size: 12pt for labels, 10pt for ticks - Always include scale bars on spatial plots - Export as both PNG (300 DPI) and SVG ## Methods Sections When writing methods text, cite the following versions: - scanpy 1.10.x - squidpy 1.4.x - anndata 0.10.x ```