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id: openst_skills_index name: OpenST Skills Index description: | Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.

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

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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