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Upstream Processing Skills Index

Coordinate upstream single-cell and spatial omics workflows from raw sequencing data to count matrices.

478|62|Updated Jul 30, 2025
Search Tags:#single-cell#pipelines#workflows#omics#spatial-omics#data-preprocessing#upstream-processing
One-click install
npx skills add https://github.com/aristoteleo/PantheonOS --skill upstream-processing-skills-index
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: Upstream Processing Skills Index
Source: https://github.com/aristoteleo/PantheonOS/tree/main/pantheon/factory/templates/skills/omics/upstream_processing
Command: npx skills add https://github.com/aristoteleo/PantheonOS --skill upstream-processing-skills-index

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Upstream Processing Skills Index centralizes and standardizes the initial data preparation workflows for single-cell and spatial omics, enabling teams to identify, assemble, and execute technology-specific preprocessing pipelines from raw sequencing data to analysis-ready matrices.

Core Features & Use Cases

  • Unified catalog of upstream pipelines (OpenST, nf-core) for raw data to counts.
  • Platform-agnostic workflows: covers barcode preprocessing, transcriptome alignment, spatial registration, segmentation, and 3D reconstruction.
  • End-to-end readiness: moves data from raw reads to analysis-ready matrices and downstream analysis readiness.
  • Real-world scenario: a team processes a Visium-like dataset with OpenST to obtain spatially-resolved gene counts ready for downstream clustering.

Quick Start

Load the desired upstream skill (OpenST or nf-core) and run its end-to-end workflow from raw data to count matrices.

Frequently Asked Questions about Upstream Processing Skills Index

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I process raw sequencing data into analysis-ready count matrices for single-cell omics?▼

This Skill standardizes upstream preprocessing workflows for single-cell and spatial omics, moving data from raw reads to analysis-ready count matrices through technology-specific pipelines including OpenST and nf-core.

What is upstream processing for spatial-omics data?▼

Upstream processing for spatial-omics coordinates multi-step workflows from raw sequencing data to count matrices, applying barcode preprocessing, spatial registration, cell segmentation, and 3D reconstruction to prepare data for downstream clustering.

How do I run an end-to-end OpenST workflow from raw reads to spatially-resolved gene counts?▼

Load the desired upstream skill like OpenST and run its end-to-end workflow to process raw data, applying spatial registration and transcriptome alignment to obtain spatially-resolved gene counts ready for analysis.

Does this upstream processing pipeline work with nf-core workflows?▼

Yes, this Skill provides a unified catalog of platform-agnostic upstream pipelines that work with nf-core, covering barcode preprocessing, transcriptome alignment, and 3D reconstruction to generate analysis-ready matrices.

What are the limitations of using a unified catalog for single-cell data preprocessing?▼

The unified catalog requires a YAML frontmatter in the root SKILL.md with at least name and description, and relies on optional directories for scripts, references, and assets to support richer context for multi-step workflows.

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