Batch Correction

HarmonyR

Fast, sensitive, and accurate integration of single-cell RNA-seq data across multiple datasets, batches, or experimental conditions.

scIB (Single-cell Integration Benchmarks)Python

A Python package for benchmarking and evaluating single-cell genomics data integration methods.

scArchesJupyter Notebook

Reference mapping for single-cell genomics

scPRINTJupyter Notebook

A large transformer foundation model for single-cell RNA sequencing data analysis, including gene network inference, denoising, and cell annotation.

MIDASPython

A PyTorch deep generative model for integrating and imputing single-cell multimodal data with missing modalities.