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Openst

Skill BioTender-max/awesome-bio-agent-skills/skills/pantheon/openst

Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.From its SKILL.md

Install
npx -y skills add BioTender-max/awesome-bio-agent-skills --skill openst

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

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SKILL.md

1.3 KB, 237 tokens by cl100k_base, as published. Nobody here has run it

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

  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

What ships with it: 1 file

19.4 KB alongside SKILL.md

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