data-engineeringdata-ai
spatial-raw-processing
Process barcoded spatial transcriptomics FASTQ pairs with st_pipeline, preserve upstream artifacts, convert the counts matrix into a standardized raw_counts.h5ad, and hand off cleanly to spatial-preprocess.
maintainer
TianGzlab
Updated 4/6/2026
Stars
115
Forks
23
quick start
Installation and usage
Process barcoded spatial transcriptomics FASTQ pairs with st_pipeline, preserve upstream artifacts, convert the counts matrix into a standardized raw_counts.h5ad, and hand off cleanly to spatial-preprocess.
Installation
$ install --globalskills.sh
Usage
Once installed, you can use this skill by running the following command in your terminal:
skills use spatial-raw-processing