# OpenST Skills Index

> Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.

- Skill: `gabrielmoreira/openst-skills-index` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add gabrielmoreira/openst-skills-index`
- Raw SKILL.md: https://api.skillmd.com/api/skills/gabrielmoreira/openst-skills-index/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: gabrielmoreira (https://skillmd.com/u/gabrielmoreira)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/gabrielmoreira/openst-skills-index

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# OpenST Skills

[Open-ST](https://rajewsky-lab.github.io/openst/) is an open-source spatial
transcriptomics method that captures transcriptome-wide expression at
sub-cellular resolution using sequencing-based spatial barcoding on
Illumina flow cells.

## Available Skills

### Computational Analysis Pipeline

Complete end-to-end computational workflow for processing Open-ST data,
covering all 6 stages from raw data to analysis-ready objects.

**Skill file**: [openst_computational.md](./openst_computational.md)

**When to use**:
- Processing raw Open-ST BCL/FASTQ files
- Running spacemake for transcriptomic alignment
- Aligning spatial coordinates to tissue images
- Segmenting cells and assigning transcripts
- Reconstructing 3D spatial data from serial sections
- Performing downstream exploratory analysis on Open-ST data

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## Using Skills

1. **Read the computational pipeline skill** for the full step-by-step workflow
2. **Follow stages sequentially**: Each stage depends on the previous one
3. **Check system requirements**: 128 GB RAM recommended, GPU for segmentation/alignment