Visium Python Packages

stpipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

biomedical-ai-skills

AI agent skills for cancer biology and multi-omics research

tangram-sc

Spatial alignment of single cell transcriptomic data.

flashdeconv

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

llm-sc-curator

Data-centric marker distillation for zero-shot cell-type and spatial annotation with LLMs.

codeconv

Perform Visium Standard Definition (SD) cell type-specific gene expression reconstruction via spot deconvolution.

cell-gps

Cell-GPS spatial topology analysis for spatial omics data.