Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells

Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

Make Complex Heatmaps

Deep probabilistic analysis of single-cell and spatial omics data

Perturbation Analysis in the scverse ecosystem.

Conditional out-of-distribution prediction

Reference mapping for single-cell genomics

Single-cell analysis in Python. Scales to >1M cells.

Spatial Single Cell Analysis in Python

An open and interoperable data framework for spatial omics data

Spatial reconstruction of dissociated single-cell data

Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data

SBMClone, a method for recovering tumor clonal composition from sparse single-cell mutation data