GNN-based cell segmentation of spatial transcriptomics data

Lightweight plotting to the terminal. 4x resolution via Unicode.

package for comparing spatial transcriptomics datasets

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

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

Single-cell perturbation analysis

Conditional out-of-distribution prediction

Reference mapping for single-cell genomics

Single-cell analysis in Python. Scales to >100M cells.

Spatial Single Cell Analysis in Python

An open and interoperable data framework for spatial omics 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