cite-seq
Deep probabilistic analysis of single-cell and spatial omics data
muon is a multimodal omics Python framework
Fast, out-of-core single-cell analysis in Python for RNA, ATAC, protein, and multi-omic data, scaling to 100M+ cells. Mount remote datasets, work within a memory budget, and trace every result through built-in provenance.
scPerturb: A resource and a python/R tool for single-cell perturbation data
Tools for single-cell feature barcoding analysis
Multi-task deep learning for cell annotation, surface-protein prediction, and joint scRNA-seq/CITE-seq embeddings.
