OpenST Skills Index
Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.
npx skills add BioTender-max/awesome-bio-agent-skills --skill openst --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 --- ## 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
- Available Skills
- Computational Analysis Pipeline
- Using Skills
What does the OpenST Skills Index skill do?
Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill openst --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.