OpenST Skills Index
- Repo stars 428
- Author repo PantheonOS
OpenST Skills
Open-ST 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
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
- Read the computational pipeline skill for the full step-by-step workflow
- Follow stages sequentially: Each stage depends on the previous one
- Check system requirements: 128 GB RAM recommended, GPU for segmentation/alignment
- Fluxly category
- Engineering
- Author-declared agents
- No explicit declaration found; this is not inferred or tested compatibility
- Static check
- 88 / 100 · heuristic scan, not runtime safety proof
- Author / version / license
- @aristoteleo · no license declared
- Fluxly token estimate
- Lean
- Fluxly setup estimate
- Plug-and-play
- External API key
- No requirement detected
- Detected OS requirements
- Unspecified
- Runtime requirements
- Unspecified
- Detected file/system behavior
-
- Read-only
- Detected network behavior
- Local-only
- Install commands
- None (reference only)
Profile is derived at build time from SKILL.md and install vectors. Subject to drift from author intent.
Heads up: 未限定 allowed-tools,默认拥有全部工具权限。
The current SKILL.md does not define a fixed output example. Available Skills
Complete end-to-end computational workflow for processing Open-ST data, covering all 6 stages from raw data to analysis-ready objects. Skill file: openstcomputational.md
Read the computational pipeline skill for the full step-by-step workflow Follow stages sequentially: Each stage depends on the previous one Check system requirements: 128 GB RAM recommended, GPU for segmentation/alignment
# 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 Author text anchors workflow facts; Fluxly only indexes current sections, terms, files, and commands.
sections -> Available Skills → Computational Analysis Pipeline → Using Skills
terms -> Skill file · When to use · Read the computational pipeline skill · Follow stages sequentially · Check system requirements
files/cmd -> rajewsky-lab.github.io/openst · openstcomputational.md · ./openstcomputational.md · BCL/FASTQ · segmentation/alignment
body sha256 -> 793c52a7c67e
Decide Fit First
Design Intent
How To Use It
Boundaries And Review