OpenST Skills Index

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

gabrielmoreira Updated 17 repo stars

File contents

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

gabrielmoreira/agent-skills-mirror/tree/main/mirrors/repos/BioTender-max@awesome-bio-agent-skills/skills/pantheon/openst commit 7e8226950e

Frequently asked questions

npx skillmds@latest add gabrielmoreira/openst-skills-index