OpenST Skills Index
- Repo stars 428
- Author updated Live
- Author repo PantheonOS
- Domain
- Engineering
- Compatible agents
-
- Claude Code
- Cursor
- Cline
- Codex
- Windsurf
- Gemini CLI
- +20
- Trust score
- 88 / 100 · community maintained
- Author / version / license
- @aristoteleo · no license declared
- Token usage
- Lean
- Setup complexity
- Plug-and-play
- External API key
- Not required
- Operating systems
- Unspecified (assume cross-platform)
- Runtime requirements
- No special requirements
- Permissions
-
- Read-only
- Write / modify
- Network behavior
- Local-only
- Install commands
- 26 variants
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。
---
name: OpenST Skills Index
description: | Open-ST is an open-source spatial transcriptomics method that captures transcriptome-wide expr…
category: engineering
runtime: no special runtime
---
# OpenST Skills Index output preview
## PART A: Task fit
- Use case: | 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. Complete end-to-end computational workflow for processing Open-ST data, runs entirely locally. Works with Claude Code, Cursor, Cline and 23 more..
- Inputs: target material, constraints, expected output, and acceptance criteria.
- Evidence boundary: follow “Available Skills / Computational Analysis Pipeline / Using Skills” and do not present inference as author intent.
## PART B: Execution result
- **01** The card summarizes the use case; runtime output centers on “| 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. Complete end-to-end computational workflow for processing Open-ST data, runs entirely locally. Works with Claude Code, Cursor, Cline and 23 more.”.
- **02** When the source has headings, the agent prioritizes “Available Skills / Computational Analysis Pipeline / Using Skills” so the result follows the author’s structure.
- **03** Typical output includes task judgment, concrete steps, required commands or file edits, validation, and follow-up options.
- **04** Risk context follows the fingerprint: read files, write/modify files; mostly runs locally; usually needs no extra API key.
## Running Rules
- read files, write/modify files; mostly runs locally; usually needs no extra API key.
- Validate with a small sample before expanding scope.
- Return the result, validation criteria, and next iteration options.The source does not require a stable slash command. After installation, invoke the skill by name and describe the task.
Name target files or source material, expected output, forbidden changes, and whether network or shell access is allowed. Permission fingerprint: read files, write/modify files.
Start with a small task and check whether the result follows “Available Skills / Computational Analysis Pipeline / Using Skills”. Inspect diffs, logs, previews, or tests before expanding scope.
Confirm the final output includes a concrete result, evidence, and next action. If it stays generic, tighten inputs, boundaries, and acceptance criteria.
---
name: OpenST Skills Index
description: | Open-ST is an open-source spatial transcriptomics method that captures transcriptome-wide expr…
category: engineering
source: aristoteleo/PantheonOS
---
# OpenST Skills Index
## When to use
- | Open-ST is an open-source spatial transcriptomics method that captures transcriptome-wide expression at sub-cellular…
- Use it when the task has clear inputs, repeatable steps, and validation criteria.
## What to provide
- Target material, scope, expected result, and forbidden changes.
- Whether network, commands, file writes, or external services are allowed.
## Execution rules
- Organize steps around “Available Skills / Computational Analysis Pipeline / Using Skills” and keep inference separate from source facts.
- read files, write/modify files; mostly runs locally; usually needs no extra API key.
- Validate with a small sample before expanding the task.
## Output requirements
- Return the deliverable, key evidence, validation method, and next action.
- Mark missing information as unknown; do not invent commands, platforms, or dependencies.The author source anchors workflow facts; repository files anchor sources and commands; Fluxly only adds fit, limitations, and quality judgment.
skill "OpenST Skills Index" {
input -> user goal + target files + boundaries + acceptance criteria
context -> Available Skills / Computational Analysis Pipeline / Using Skills
rules -> SKILL.md triggers / order / output contract
runtime -> no special runtime | read files, write/modify files | mostly runs locally
guardrails -> usually needs no extra API key + small-sample validation + diff/log review
output -> copyable result + checklist + next iteration
}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
Decide Fit First
Design Intent
How To Use It
Boundaries And Review