Visium Python Packages

tangram-sc

Spatial alignment of single cell transcriptomic data.

flashdeconv

Fast spatial deconvolution via leverage-score sketching — scales to million-spot datasets while preserving rare cell type signals.

llm-sc-curator

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

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.

oncoordinate

Oncoordinate is an interpretable deep learning framework for single-cell and spatial transcriptomic analysis of malignancy that learns malignant and malignancy-associated cell states across epithelial, stromal, and immune lineages while remaining tightly integrated with the scverse ecosystem.