Fig. 1. Single-cell analysis across modalities.

Cellular state is characterized by various modalities, including, but not limited to, RNA transcription, chromatin accessibility, surface proteins including T cell receptors (TCRs) and B cell receptors (BCRs), as well as spatial location. Various frameworks covering the most important analysis steps have been developed. Transcriptomics data can be analysed with Scanpy⁴, Seurat³⁶ and Bioconductor-based SingleCellExperiment²; chromatin accessibility measurements with muon¹⁵⁰, ArchR¹⁴⁰, snapATAC¹³⁵ and Signac¹⁴³; TCR and BCR repertoire analysis with Scirpy¹⁶⁴, Dandelion¹⁴ and scRepertoire¹⁶⁶; surface protein expression with muon¹⁵⁰, Seurat³⁶ and CiteFuse¹⁶³; spatially resolved single-cell data sets with frameworks such as Squidpy²⁰⁹, Seurat³⁶, Giotto²⁴⁴ and Bioconductor-based SpatialExperiment²¹¹. These frameworks are complemented with a myriad of additional tools for specific subsequent analysis tasks.