OpenST Skills Index: Анализ данных пространственной транскриптомики

--- 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](https://rajewsky-lab.github.io/openst/) 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](./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