Upstream Processing Skills Index
OfficialOrchestrate upstream omics data preprocessing.
Data & Analytics#single-cell#pipelines#workflows#omics#spatial-omics#data-preprocessing#upstream-processing
Authoraristoteleo
Version1.0.0
Installs0
System Documentation
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.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: Upstream Processing Skills Index Download link: https://github.com/aristoteleo/PantheonOS/archive/main.zip#upstream-processing-skills-index Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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