Latch Skills

Skills for building on the Latch platform using any agent environment that supports the Claude Agent SDK skill format — including Claude Code, OpenAI Codex, Latch Plots, and custom agent setups.

Each skill is a directory containing a SKILL.md file with YAML frontmatter (name, description) and complete API reference documentation that the agent loads on demand.

Skills

Skill	Description
latch-data-access	Browse and select files from Latch Data, Registry tables, and DataFrames. Includes LPath utilities for working with latch:// paths.
latch-plots-ui	Render plots, tables, AnnData viewers, IGV browsers, and interactive input widgets in Latch Plots notebooks.
latch-workflows	Launch and monitor bioinformatics workflows on Latch from agent code — including parameter construction, validation, and output retrieval.
latch-curation	Curate external datasets (GEO/GSE, collaborator uploads) into Latch-compatible AnnData with Ensembl gene IDs and ontology-annotated metadata. Includes GEO download, gene ID conversion, and validation libraries.
takara-devkit	Analyze Takara Seeker/Trekker spatial transcriptomics data — QC, background removal, normalization, clustering, differential expression, and cell typing.
vizgen-devkit	Analyze Vizgen MERFISH spatial transcriptomics data — cell segmentation, preprocessing, QC, spatial analysis, and secondary analysis.
xenium-devkit	Analyze 10x Genomics Xenium in situ data — data preparation, preprocessing, differential expression, cell type annotation, and domain detection.
atlasx-devkit	Analyze AtlasXomics spatial epigenomics (ATAC-seq) data — QC, clustering, differential analysis, and cell type annotation.

Getting started

Clone this repo into your .claude/skills/ directory (or let your agent environment handle it automatically):

git clone https://github.com/latchbio/latch-skills.git .claude/skills/latch-skills

For monorepos like this one, each subdirectory with a SKILL.md is treated as an independent skill. Symlink them individually if your agent expects flat skill directories:

for dir in .claude/skills/latch-skills/*/; do
  ln -s "$dir" ".claude/skills/$(basename "$dir")"
done

Adding a new skill

Create a directory with a SKILL.md:

---
name: my-skill
description: >
  When to load this skill.
---

# My Skill

Reference documentation here.

Structure

latch-skills/
├── atlasx-devkit/
│   └── SKILL.md, steps/, wf/
├── latch-curation/
│   ├── SKILL.md
│   └── lib/curate/
├── latch-data-access/
│   └── SKILL.md
├── latch-plots-ui/
│   └── SKILL.md
├── latch-workflows/
│   └── SKILL.md
├── takara-devkit/
│   └── SKILL.md, steps/, wf/, lib/
├── vizgen-devkit/
│   └── SKILL.md, steps/, wf/
└── xenium-devkit/
    └── SKILL.md, steps/, wf/, lib/