Curated single cell multimodal landmark datasets for R/Bioconductor

Background: The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes. Results: We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T. We integrate data modalities via the MultiAssayExperiment Bioconductor class, document and re-distribute datasets as the SingleCellMultiModal package in Bioconductor’s Cloud-based ExperimentHub. The result is single-command actualization of landmark datasets from seven single-cell multimodal data generation technologies, without need for further data processing or wrangling in order to analyze and develop methods within Bioconductor’s ecosystem of hundreds of packages for single-cell and multimodal data. Conclusions: We provide two examples of integrative analyses that are greatly simplified by SingleCellMultiModal. The package will facilitate development of bioinformatic and statistical methods in Bioconductor to meet the challenges of integrating molecular layers and analyzing phenotypic outputs including cell differentiation, activity, and disease. Author summary: Experimental data packages that provide landmark datasets have historically played an important role in the development of new statistical methods in Bioconductor by lowering the barrier of access to relevant data, providing a common testing ground for software development and benchmarking, and encouraging interoperability around common data structures. In this manuscript, we review major classes of technologies for collecting multimodal data including genomics, transcriptomics, epigenetics, proteomics, and spatial information at the level of single cells. We present the SingleCellMultiModal R/Bioconductor package that provides single-command access to landmark datasets from seven different technologies, storing datasets using HDF5 and sparse arrays for memory efficiency and integrating data modalities via the MultiAssayExperiment class. We demonstrate two integrative analyses that are greatly simplified by SingleCellMultiModal. The package facilitates development and benchmarking of bioinformatic and statistical methods to integrate molecular layers at the level of single cells with phenotypic outputs including cell differentiation, activity, and disease, within Bioconductor’s ecosystem of hundreds of packages for single-cell and multimodal data.